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Huifang Jiang
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China

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Journal article
Published: 06 July 2021 in International Journal of Molecular Sciences
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Sucrose content is a crucial indicator of quality and flavor in peanut seed, and there is a lack of clarity on the molecular basis of sucrose metabolism in peanut seed. In this context, we performed a comprehensive comparative transcriptome study on the samples collected at seven seed development stages between a high-sucrose content variety (ICG 12625) and a low-sucrose content variety (Zhonghua 10). The transcriptome analysis identified a total of 8334 genes exhibiting significantly different abundances between the high- and low-sucrose varieties. We identified 28 differentially expressed genes (DEGs) involved in sucrose metabolism in peanut and 12 of these encoded sugars will eventually be exported transporters (SWEETs). The remaining 16 genes encoded enzymes, such as cell wall invertase (CWIN), vacuolar invertase (VIN), cytoplasmic invertase (CIN), cytosolic fructose-bisphosphate aldolase (FBA), cytosolic fructose-1,6-bisphosphate phosphatase (FBP), sucrose synthase (SUS), cytosolic phosphoglucose isomerase (PGI), hexokinase (HK), and sucrose-phosphate phosphatase (SPP). The weighted gene co-expression network analysis (WGCNA) identified seven genes encoding key enzymes (CIN, FBA, FBP, HK, and SPP), three SWEET genes, and 90 transcription factors (TFs) showing a high correlation with sucrose content. Furthermore, upon validation, six of these genes were successfully verified as exhibiting higher expression in high-sucrose recombinant inbred lines (RILs). Our study suggested the key roles of the high expression of SWEETs and enzymes in sucrose synthesis making the genotype ICG 12625 sucrose-rich. This study also provided insights into the molecular basis of sucrose metabolism during seed development and facilitated exploring key candidate genes and molecular breeding for sucrose content in peanuts.

ACS Style

Weitao Li; Li Huang; Nian Liu; Manish Pandey; Yuning Chen; Liangqiang Cheng; Jianbin Guo; Bolun Yu; Huaiyong Luo; Xiaojing Zhou; Dongxin Huai; Weigang Chen; Liying Yan; Xin Wang; Yong Lei; Rajeev Varshney; Boshou Liao; Huifang Jiang. Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts. International Journal of Molecular Sciences 2021, 22, 7266 .

AMA Style

Weitao Li, Li Huang, Nian Liu, Manish Pandey, Yuning Chen, Liangqiang Cheng, Jianbin Guo, Bolun Yu, Huaiyong Luo, Xiaojing Zhou, Dongxin Huai, Weigang Chen, Liying Yan, Xin Wang, Yong Lei, Rajeev Varshney, Boshou Liao, Huifang Jiang. Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts. International Journal of Molecular Sciences. 2021; 22 (14):7266.

Chicago/Turabian Style

Weitao Li; Li Huang; Nian Liu; Manish Pandey; Yuning Chen; Liangqiang Cheng; Jianbin Guo; Bolun Yu; Huaiyong Luo; Xiaojing Zhou; Dongxin Huai; Weigang Chen; Liying Yan; Xin Wang; Yong Lei; Rajeev Varshney; Boshou Liao; Huifang Jiang. 2021. "Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts." International Journal of Molecular Sciences 22, no. 14: 7266.

Preprint content
Published: 07 June 2021
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Cultivated peanut (Arachis hypogaea L.) is rich in edible oil and protein, which is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanut, hindering the development of peanut industry and threatening consumers’ health. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for control the aflatoxin contamination, and understanding of the genetic basis of resistance is vital to its genetic enhancement. In this study, we report the QTL mapping of resistance to A. flavus infection of a well-known resistant variety J11. A recombination inbred line (RIL) population was constructed by crossing a susceptible variety Zhonghua 16 and J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of infection index in four consecutive years, six novel resistant QTLs were identified and they explained 5.03-10.87% phenotypic variances. The favorable alleles of five QTLs were from J11 while that of one QTL were from Zhonghua 16. The pyramiding of these favorable alleles significantly improved the resistance to A. flavus infection. These results could contribute greatly to understanding of genetic basis of A. flavus resistance and could be meaningful in further resistance improvement in peanut.

ACS Style

Yifei Jiang; Huaiyong Luo; Bolun Yu; Yingbin Ding; Yanping Kang; Li Huang; Xiaojing Zhou; Nian Liu; Weigang Chen; Jianbin Guo; Dongxin Huai; Yong Lei; Huifang Jiang; Liying Yan; Boshou Liao. High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping Qtls of Resistance to Aspergillus Flavus Infection in Peanut. 2021, 1 .

AMA Style

Yifei Jiang, Huaiyong Luo, Bolun Yu, Yingbin Ding, Yanping Kang, Li Huang, Xiaojing Zhou, Nian Liu, Weigang Chen, Jianbin Guo, Dongxin Huai, Yong Lei, Huifang Jiang, Liying Yan, Boshou Liao. High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping Qtls of Resistance to Aspergillus Flavus Infection in Peanut. . 2021; ():1.

Chicago/Turabian Style

Yifei Jiang; Huaiyong Luo; Bolun Yu; Yingbin Ding; Yanping Kang; Li Huang; Xiaojing Zhou; Nian Liu; Weigang Chen; Jianbin Guo; Dongxin Huai; Yong Lei; Huifang Jiang; Liying Yan; Boshou Liao. 2021. "High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping Qtls of Resistance to Aspergillus Flavus Infection in Peanut." , no. : 1.

Research article
Published: 28 January 2021 in Euphytica
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Peanut is one of major sources for vegetable oil. Improving oil content is an important goal for peanut breeding programs. Major loci with linked markers for oil content could facilitate rapid development of high-oil varieties through marker-assisted breeding. To identify major loci underlying the oil content, we conducted the QTL analysis based on the high-dense genetic map, using RIL population derived from Zhonghua10 and ICG12625. A total of 18 additive QTLs, including two major and stable QTLs (qOCB06 and qOCB10.1), were identified in three environments. Besides, 26 pairs of QTLs with epistatic (additive × additive) interaction were mapped on 17 linkage groups. qOCB06 with up to 22.59% of the phenotypic variations was located in a 0.6-Mb interval of B06. qOCB10.1 on B10 explained 9.18–12.55% of the phenotypic variations. The additive effect of two QTLs ranged from 0.70 to 1.13% oil content in different environments. Favorable alleles of the two loci were from male and female parent, respectively. Pyramiding the two favorable alleles in the RIL population could increase “2.66 ± 0.48%” oil content across multiple environments. The marker Ai06B29452 and AGGS2133-1 linked to qOCB06 and qOCB10.1, respectively, were validated to be associated with oil content in peanut germplasms with diverse phenotypes. These markers were valuable in marker-assisted selection and pyramiding breeding for improving oil content in peanut. Major and stable QTLs with linked markers in the present study provided resources to discovery candidate genes in the future and to guide marker-assisted selection for improving oil content in peanut.

ACS Style

Jianbin Guo; Nian Liu; Weitao Li; Bei Wu; Haiwen Chen; Li Huang; Weigang Chen; Huaiyong Luo; Xiaojing Zhou; Huifang Jiang. Identification of two major loci and linked marker for oil content in peanut (Arachis hypogaea L.). Euphytica 2021, 217, 1 -11.

AMA Style

Jianbin Guo, Nian Liu, Weitao Li, Bei Wu, Haiwen Chen, Li Huang, Weigang Chen, Huaiyong Luo, Xiaojing Zhou, Huifang Jiang. Identification of two major loci and linked marker for oil content in peanut (Arachis hypogaea L.). Euphytica. 2021; 217 (2):1-11.

Chicago/Turabian Style

Jianbin Guo; Nian Liu; Weitao Li; Bei Wu; Haiwen Chen; Li Huang; Weigang Chen; Huaiyong Luo; Xiaojing Zhou; Huifang Jiang. 2021. "Identification of two major loci and linked marker for oil content in peanut (Arachis hypogaea L.)." Euphytica 217, no. 2: 1-11.

Journal article
Published: 08 June 2020 in BMC Genetics
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Background Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in several peanut breeding programs of the world. Tightly linked markers are required for faster development of high oil content peanut varieties through genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of such associated markers. Results An association mapping panel consisting of 292 peanut varieties extensively distributed in China was phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The structure, phylogenetic relationship, and principal component analysis (PCA) indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers (AGGS1014_2 and AHGS0798) with 6.90–9.94% PVE were verified to enhance oil content in an independent RIL population and also indicated selection during the breeding program. Conclusion This study provided insights into the genetic basis of oil content in peanut and verified highly associated two SSR markers to facilitate marker-assisted selection for developing high-oil content breeding peanut varieties.

ACS Style

Nian Liu; Li Huang; Weigang Chen; Bei Wu; Manish K. Pandey; Huaiyong Luo; Xiaojing Zhou; Jianbin Guo; Haiwen Chen; Dongxin Huai; Yuning Chen; Yong Lei; Boshou Liao; Xiaoping Ren; Rajeev K. Varshney; Huifang Jiang. Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping. BMC Genetics 2020, 21, 1 -12.

AMA Style

Nian Liu, Li Huang, Weigang Chen, Bei Wu, Manish K. Pandey, Huaiyong Luo, Xiaojing Zhou, Jianbin Guo, Haiwen Chen, Dongxin Huai, Yuning Chen, Yong Lei, Boshou Liao, Xiaoping Ren, Rajeev K. Varshney, Huifang Jiang. Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping. BMC Genetics. 2020; 21 (1):1-12.

Chicago/Turabian Style

Nian Liu; Li Huang; Weigang Chen; Bei Wu; Manish K. Pandey; Huaiyong Luo; Xiaojing Zhou; Jianbin Guo; Haiwen Chen; Dongxin Huai; Yuning Chen; Yong Lei; Boshou Liao; Xiaoping Ren; Rajeev K. Varshney; Huifang Jiang. 2020. "Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping." BMC Genetics 21, no. 1: 1-12.

Preprint content
Published: 29 May 2020
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Background: Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in several peanut breeding programs of the world. Tightly linked markers are required for faster development of high oil content peanut varieties through genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of such associated markers. Results: An association mapping panel consisting of 292 peanut varieties extensively distributed in China was phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The structure, phylogenetic relationship, and principal component analysis (PCA) indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers (AGGS1014_2 and AHGS0798) with 6.90-9.94% PVE were verified to enhance oil content in an independent RIL population and also indicated selection during the breeding program. Conclusion: This study provided insights into the genetic basis of oil content in peanut and verified highly associated two SSR markers to facilitate marker-assisted selection for developing high-oil content breeding peanut varieties.

ACS Style

Nian Liu; Li Huang; Weigang Chen; Bei Wu; Manish K. Pandey; Huaiyong Luo; Xiaojing Zhou; Jianbin Guo; Haiwen Chen; Dongxin Huai; Yuning Chen; Yong Lei; Boshou Liao; Xiaoping Ren; Rajeev K. Varshney; Huifang Jiang. Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping. 2020, 1 .

AMA Style

Nian Liu, Li Huang, Weigang Chen, Bei Wu, Manish K. Pandey, Huaiyong Luo, Xiaojing Zhou, Jianbin Guo, Haiwen Chen, Dongxin Huai, Yuning Chen, Yong Lei, Boshou Liao, Xiaoping Ren, Rajeev K. Varshney, Huifang Jiang. Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping. . 2020; ():1.

Chicago/Turabian Style

Nian Liu; Li Huang; Weigang Chen; Bei Wu; Manish K. Pandey; Huaiyong Luo; Xiaojing Zhou; Jianbin Guo; Haiwen Chen; Dongxin Huai; Yuning Chen; Yong Lei; Boshou Liao; Xiaoping Ren; Rajeev K. Varshney; Huifang Jiang. 2020. "Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping." , no. : 1.

Research article
Published: 13 March 2020 in Plant Biotechnology Journal
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Spatio‐temporal and developmental stage specific transcriptome analysis play a crucial role in systems biology‐based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world’s widest cultivated subsp. fastigiata based on RNA‐seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired‐end filtered reads were generated followed by identification of 81,901 transcripts from an early maturing, high‐yielding, drought tolerant groundnut variety, ICGV 91114. Further, 57,344 genome‐wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in‐depth analysis of the global transcriptome sheds light into complex regulatory networks namely, gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer‐friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits.

ACS Style

Pallavi Sinha; Prasad Bajaj; Lekha T. Pazhamala; Spurthi N. Nayak; Manish K. Pandey; Annapurna Chitikineni; Dongxin Huai; Aamir W. Khan; Aarthi Desai; Huifang Jiang; Weijian Zhuang; Baozhu Guo; Boshou Liao; Rajeev K. Varshney. Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications. Plant Biotechnology Journal 2020, 18, 2187 -2200.

AMA Style

Pallavi Sinha, Prasad Bajaj, Lekha T. Pazhamala, Spurthi N. Nayak, Manish K. Pandey, Annapurna Chitikineni, Dongxin Huai, Aamir W. Khan, Aarthi Desai, Huifang Jiang, Weijian Zhuang, Baozhu Guo, Boshou Liao, Rajeev K. Varshney. Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications. Plant Biotechnology Journal. 2020; 18 (11):2187-2200.

Chicago/Turabian Style

Pallavi Sinha; Prasad Bajaj; Lekha T. Pazhamala; Spurthi N. Nayak; Manish K. Pandey; Annapurna Chitikineni; Dongxin Huai; Aamir W. Khan; Aarthi Desai; Huifang Jiang; Weijian Zhuang; Baozhu Guo; Boshou Liao; Rajeev K. Varshney. 2020. "Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications." Plant Biotechnology Journal 18, no. 11: 2187-2200.

Preprint content
Published: 13 March 2020
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Background Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in these peanut breeding programs. Linked markers for oil content is required for use in genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of associated markers. Results An association mapping panel consisting of 292 peanut varieties extensively distributed in China were phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The results of structure, phylogenetic relationship, and PCA analyses indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis using genetic and phenotypic data identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers AGGS1014_2 and AHGS0798 with 6.90-9.94% PVE were verified to enhance oil content in an independent RIL population. The combined genotypes of AGGS1014_2 and AHGS0798 appeared to experience selection during the breeding program. Conclusion This study provided insights into the genetic basis of oil content in peanut and verified that two SSR markers were highly associated with oil content. Our results could facilitate marker-assisted selection for high-oil content breeding.

ACS Style

Nian Liu; Li Huang; Weigang Chen; Bei Wu; Manish K. Pandey; Huaiyong Luo; Xiaojing Zhou; Jianbin Guo; Haiwen Chen; Dongxin Huai; Yuning Chen; Yong Lei; Boshou Liao; Xiaoping Ren; Rajeev K. Varshney; Huifang Jiang. Dissection of the genetic basis of oil content in Chinese peanut cultivars by association mapping. 2020, 1 .

AMA Style

Nian Liu, Li Huang, Weigang Chen, Bei Wu, Manish K. Pandey, Huaiyong Luo, Xiaojing Zhou, Jianbin Guo, Haiwen Chen, Dongxin Huai, Yuning Chen, Yong Lei, Boshou Liao, Xiaoping Ren, Rajeev K. Varshney, Huifang Jiang. Dissection of the genetic basis of oil content in Chinese peanut cultivars by association mapping. . 2020; ():1.

Chicago/Turabian Style

Nian Liu; Li Huang; Weigang Chen; Bei Wu; Manish K. Pandey; Huaiyong Luo; Xiaojing Zhou; Jianbin Guo; Haiwen Chen; Dongxin Huai; Yuning Chen; Yong Lei; Boshou Liao; Xiaoping Ren; Rajeev K. Varshney; Huifang Jiang. 2020. "Dissection of the genetic basis of oil content in Chinese peanut cultivars by association mapping." , no. : 1.

Journal article
Published: 01 March 2020 in Toxins
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Aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) are the most common aflatoxins produced by Aspergillus flavus in peanuts, with high carcinogenicity and teratogenicity. Identification of DNA markers associated with resistance to aflatoxin production is likely to offer breeders efficient tools to develop resistant cultivars through molecular breeding. In this study, seeds of 99 accessions of a Chinese peanut mini-mini core collection were investigated for their reaction to aflatoxin production by a laboratory kernel inoculation assay. Two resistant accessions (Zh.h0551 and Zh.h2150) were identified, with their aflatoxin content being 8.11%–18.90% of the susceptible control. The 99 peanut accessions were also genotyped by restriction site-associated DNA sequencing (RAD-Seq) for a genome-wide association study (GWAS). A total of 60 SNP (single nucleotide polymorphism) markers associated with aflatoxin production were detected, and they explained 16.87%–31.70% of phenotypic variation (PVE), with SNP02686 and SNP19994 possessing 31.70% and 28.91% PVE, respectively. Aflatoxin contents of accessions with “AG” (existed in Zh.h0551 and Zh.h2150) and “GG” genotypes of either SNP19994 or SNP02686 were significantly lower than that of “AA” genotypes in the mean value of a three-year assay. The resistant accessions and molecular markers identified in this study are likely to be helpful for deployment in aflatoxin resistance breeding in peanuts.

ACS Style

Bolun Yu; Huifang Jiang; Manish K. Pandey; Li Huang; Dongxin Huai; Xiaojing Zhou; Yanping Kang; Rajeev K. Varshney; Hari K. Sudini; Xiaoping Ren; Huaiyong Luo; Nian Liu; Weigang Chen; Jianbin Guo; Weitao Li; Yingbin Ding; Yifei Jiang; Yong Lei; Boshou Liao. Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance. Toxins 2020, 12, 156 .

AMA Style

Bolun Yu, Huifang Jiang, Manish K. Pandey, Li Huang, Dongxin Huai, Xiaojing Zhou, Yanping Kang, Rajeev K. Varshney, Hari K. Sudini, Xiaoping Ren, Huaiyong Luo, Nian Liu, Weigang Chen, Jianbin Guo, Weitao Li, Yingbin Ding, Yifei Jiang, Yong Lei, Boshou Liao. Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance. Toxins. 2020; 12 (3):156.

Chicago/Turabian Style

Bolun Yu; Huifang Jiang; Manish K. Pandey; Li Huang; Dongxin Huai; Xiaojing Zhou; Yanping Kang; Rajeev K. Varshney; Hari K. Sudini; Xiaoping Ren; Huaiyong Luo; Nian Liu; Weigang Chen; Jianbin Guo; Weitao Li; Yingbin Ding; Yifei Jiang; Yong Lei; Boshou Liao. 2020. "Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance." Toxins 12, no. 3: 156.

Original article
Published: 24 January 2020 in Theoretical and Applied Genetics
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Key message Two novel and adjacent genomics and candidate genes for bacterial wilt resistance were identified on chromosome B02 in peanut variety Zhonghua 6 using both traditional QTL mapping and QTL-seq methods. Abstract Peanut (Arachis hypogaea) is an important oilseed crop worldwide. Utilization of genetic resistance is the most economic and effective approach to control bacterial wilt, one of the most devastating plant diseases, in peanut production. To accelerate the genetic improvement of bacterial wilt resistance (BWR) in peanut breeding programs, quantitative trait locus (QTL) mapping has been conducted for two resistant varieties. In this context, we deployed linkage mapping as well as sequencing-based mapping approach, QTL-seq, to identify genomic regions and candidate genes for BWR in another highly resistant variety Zhonghua 6. The recombination inbred line population (268 progenies) from the cross Xuhua 13 × Zhonghua 6 was used in BWR evaluation across five environments. QTL mapping using both SSR- and SNP-based genetic maps identified a stable QTL (qBWRB02-1) on chromosome B02 with 37.79–78.86% phenotypic variation explained (PVE) across five environments. The QTL-seq facilitated further dissection of qBWRB02-1 into two adjacent genomic regions, qBWRB02-1-1 (2.81–4.24 Mb) and qBWRB02-1-2 (6.54–8.75 Mb). Mapping of newly developed Kompetitive allele-specific PCR (KASP) markers on the genetic map confirmed their stable expressions across five environments. The effects of qBWRB02-1-1 (49.43–68.86% PVE) were much higher than qBWRB02-1-2 (3.96–6.48% PVE) and other previously reported QTLs. Nineteen putative candidate genes affected by 49 non-synonymous SNPs were identified for qBWRB02-1-1, and ten of them were predicted to code for disease resistance proteins. The major and stable QTL qBWRB02-1-1 and validated KASP markers could be deployed in genomics-assisted breeding (GAB) to develop improved peanut varieties with enhanced BWR.

ACS Style

Huaiyong Luo; Manish K. Pandey; Ye Zhi; Huan Zhang; Siliang Xu; Jianbin Guo; Bei Wu; Haiwen Chen; Xiaoping Ren; Xiaojing Zhou; Yuning Chen; Weigang Chen; Li Huang; Nian Liu; Hari K. Sudini; Rajeev K. Varshney; Yong Lei; Boshou Liao; Huifang Jiang. Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6. Theoretical and Applied Genetics 2020, 133, 1133 -1148.

AMA Style

Huaiyong Luo, Manish K. Pandey, Ye Zhi, Huan Zhang, Siliang Xu, Jianbin Guo, Bei Wu, Haiwen Chen, Xiaoping Ren, Xiaojing Zhou, Yuning Chen, Weigang Chen, Li Huang, Nian Liu, Hari K. Sudini, Rajeev K. Varshney, Yong Lei, Boshou Liao, Huifang Jiang. Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6. Theoretical and Applied Genetics. 2020; 133 (4):1133-1148.

Chicago/Turabian Style

Huaiyong Luo; Manish K. Pandey; Ye Zhi; Huan Zhang; Siliang Xu; Jianbin Guo; Bei Wu; Haiwen Chen; Xiaoping Ren; Xiaojing Zhou; Yuning Chen; Weigang Chen; Li Huang; Nian Liu; Hari K. Sudini; Rajeev K. Varshney; Yong Lei; Boshou Liao; Huifang Jiang. 2020. "Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6." Theoretical and Applied Genetics 133, no. 4: 1133-1148.

Research article
Published: 09 January 2020 in Journal of Separation Science
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Resveratrol, a stilbene phytoalexin in plants, is believed to benefit human health. In this study, an optimized enzyme-assisted method was developed to extract the total content of trans-resveratrol (free or combined with glucose) in peanut seeds, followed by detection using high-performance liquid chromatography. The extraction process was optimized by Box-Behnken design and response surface methodology. The optimized enzyme concentration, digestion time, pH, and temperature were 3.02 g/L, 57.06 min, 5.88, and 51.05°C, respectively. Validation tests indicated that the experimental yield of trans-resveratrol was 0.183 ± 0.007 µg/g with a relative standard deviation of 3.87% (n = 5) under the optimal condition, which was closely agreed with the predicted value (0.182 µg/g). The recoveries obtained from the spiked samples were varied from 89.4 to 103.9%. Therefore, this study will provide a useful method for quantification of total trans-resveratrol in peanut seeds.

ACS Style

Siliang Xu; Huaiyong Luo; Haiwen Chen; Jianbin Guo; Bolun Yu; Huan Zhang; Weitao Li; Weigang Chen; Xiaojin Zhou; Li Huang; Nian Liu; Yong Lei; Boshou Liao; Huifang Jiang. Optimization of extraction of total trans ‐resveratrol from peanut seeds and its determination by HPLC. Journal of Separation Science 2020, 43, 1024 -1031.

AMA Style

Siliang Xu, Huaiyong Luo, Haiwen Chen, Jianbin Guo, Bolun Yu, Huan Zhang, Weitao Li, Weigang Chen, Xiaojin Zhou, Li Huang, Nian Liu, Yong Lei, Boshou Liao, Huifang Jiang. Optimization of extraction of total trans ‐resveratrol from peanut seeds and its determination by HPLC. Journal of Separation Science. 2020; 43 (6):1024-1031.

Chicago/Turabian Style

Siliang Xu; Huaiyong Luo; Haiwen Chen; Jianbin Guo; Bolun Yu; Huan Zhang; Weitao Li; Weigang Chen; Xiaojin Zhou; Li Huang; Nian Liu; Yong Lei; Boshou Liao; Huifang Jiang. 2020. "Optimization of extraction of total trans ‐resveratrol from peanut seeds and its determination by HPLC." Journal of Separation Science 43, no. 6: 1024-1031.

Original article
Published: 26 September 2019 in Theoretical and Applied Genetics
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Key message ddRAD-seq-based high-density genetic map comprising 2595 loci identified a major and consensus QTL with a linked marker in a 0.8-Mb physical interval for oil content in peanut. Abstract Enhancing oil content is an important breeding objective in peanut. High-resolution mapping of quantitative trait loci (QTLs) with linked markers could facilitate marker-assisted selection in breeding for target traits. In the present study, a recombined inbred line population (Xuhua 13 × Zhonghua 6) was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing (ddRAD-seq). The resulting high-density genetic map contained 2595 loci, and spanned a length of 2465.62 cM, with an average distance of 0.95 cM/locus. Seven QTLs for oil content were identified on five linkage groups, including the major and stable QTL qOCA08.1 on chromosome A08 with 10.14–27.19% phenotypic variation explained. The physical interval of qOCA08.1 was further delimited to a ~ 0.8-Mb genomic region where two genes affecting oil synthesis had been annotated. The marker SNPOCA08 was developed targeting the SNP loci associated with oil content and validated in peanut cultivars with diverse oil contents. The major and stable QTL identified in the present study could be further dissected for gene discovery. Furthermore, the tightly linked marker for oil content would be useful in marker-assisted breeding in peanut.

ACS Style

Nian Liu; Jianbin Guo; Xiaojing Zhou; Bei Wu; Li Huang; Huaiyong Luo; Yuning Chen; Weigang Chen; Yong Lei; Yi Huang; Boshou Liao; Huifang Jiang. High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.). Theoretical and Applied Genetics 2019, 133, 37 -49.

AMA Style

Nian Liu, Jianbin Guo, Xiaojing Zhou, Bei Wu, Li Huang, Huaiyong Luo, Yuning Chen, Weigang Chen, Yong Lei, Yi Huang, Boshou Liao, Huifang Jiang. High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.). Theoretical and Applied Genetics. 2019; 133 (1):37-49.

Chicago/Turabian Style

Nian Liu; Jianbin Guo; Xiaojing Zhou; Bei Wu; Li Huang; Huaiyong Luo; Yuning Chen; Weigang Chen; Yong Lei; Yi Huang; Boshou Liao; Huifang Jiang. 2019. "High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.)." Theoretical and Applied Genetics 133, no. 1: 37-49.

Research article
Published: 30 August 2019 in Plant Biotechnology Journal
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The transcriptome connects genome to the gene function and ultimate phenome in biology. So far transcriptomic approach was not used in peanut for performing trait mapping in bi‐parental populations. In this research, we sequenced the whole‐transcriptome in immature seeds in a peanut recombinant inbred line (RIL) population and explored thoroughly the landscape of transcriptomic variations and its genetic basis. The comprehensive analysis identified total 49,691 genes in RIL population, of which 92 genes followed a paramutation‐like expression pattern. Expression quantitative trait loci (eQTL) analysis identified 1,207 local eQTLs and 15,837 distant eQTLs contributing to the whole‐genome transcriptomic variation in peanut. There were 94 eQTL hotspot regions detected across the genome with the dominance of distant eQTL. By integrating transcriptomic profile and annotation analyses, we unveiled a putative candidate gene and developed a linked marker InDel02 underlying a major QTL responsible for purple testa color in peanut. Our result provided a first understanding of genetic basis of whole transcriptomic variation in peanut and illustrates the potential of the transcriptome‐aid approach in dissecting important traits in non‐model plants. This article is protected by copyright. All rights reserved.

ACS Style

Li Huang; Xia Liu; Manish K. Pandey; Xiaoping Ren; Haiwen Chen; Xiaomeng Xue; Nian Liu; Dongxin Huai; Yuning Chen; Xiaojing Zhou; Huaiyong Luo; Weigang Chen; Yong Lei; Kede Liu; Yingjie Xiao; Rajeev K. Varshney; Boshou Liao; Huifang Jiang. Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut. Plant Biotechnology Journal 2019, 18, 779 -790.

AMA Style

Li Huang, Xia Liu, Manish K. Pandey, Xiaoping Ren, Haiwen Chen, Xiaomeng Xue, Nian Liu, Dongxin Huai, Yuning Chen, Xiaojing Zhou, Huaiyong Luo, Weigang Chen, Yong Lei, Kede Liu, Yingjie Xiao, Rajeev K. Varshney, Boshou Liao, Huifang Jiang. Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut. Plant Biotechnology Journal. 2019; 18 (3):779-790.

Chicago/Turabian Style

Li Huang; Xia Liu; Manish K. Pandey; Xiaoping Ren; Haiwen Chen; Xiaomeng Xue; Nian Liu; Dongxin Huai; Yuning Chen; Xiaojing Zhou; Huaiyong Luo; Weigang Chen; Yong Lei; Kede Liu; Yingjie Xiao; Rajeev K. Varshney; Boshou Liao; Huifang Jiang. 2019. "Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut." Plant Biotechnology Journal 18, no. 3: 779-790.

Review
Published: 03 June 2019 in Toxins
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Aflatoxin is considered a “hidden poison” due to its slow and adverse effect on various biological pathways in humans, particularly among children, in whom it leads to delayed development, stunted growth, liver damage, and liver cancer. Unfortunately, the unpredictable behavior of the fungus as well as climatic conditions pose serious challenges in precise phenotyping, genetic prediction and genetic improvement, leaving the complete onus of preventing aflatoxin contamination in crops on post-harvest management. Equipping popular crop varieties with genetic resistance to aflatoxin is key to effective lowering of infection in farmer’s fields. A combination of genetic resistance for in vitro seed colonization (IVSC), pre-harvest aflatoxin contamination (PAC) and aflatoxin production together with pre- and post-harvest management may provide a sustainable solution to aflatoxin contamination. In this context, modern “omics” approaches, including next-generation genomics technologies, can provide improved and decisive information and genetic solutions. Preventing contamination will not only drastically boost the consumption and trade of the crops and products across nations/regions, but more importantly, stave off deleterious health problems among consumers across the globe.

ACS Style

Manish K. Pandey; Rakesh Kumar; Arun K. Pandey; Pooja Soni; Sunil S. Gangurde; Hari K. Sudini; Jake C. Fountain; Boshou Liao; Haile Desmae; Patrick Okori; Xiaoping Chen; Huifang Jiang; Venugopal Mendu; Hamidou Falalou; Samuel Njoroge; James Mwololo; Baozhu Guo; Weijian Zhuang; Xingjun Wang; Xuanqiang Liang; Rajeev K. Varshney. Mitigating Aflatoxin Contamination in Groundnut through A Combination of Genetic Resistance and Post-Harvest Management Practices. Toxins 2019, 11, 315 .

AMA Style

Manish K. Pandey, Rakesh Kumar, Arun K. Pandey, Pooja Soni, Sunil S. Gangurde, Hari K. Sudini, Jake C. Fountain, Boshou Liao, Haile Desmae, Patrick Okori, Xiaoping Chen, Huifang Jiang, Venugopal Mendu, Hamidou Falalou, Samuel Njoroge, James Mwololo, Baozhu Guo, Weijian Zhuang, Xingjun Wang, Xuanqiang Liang, Rajeev K. Varshney. Mitigating Aflatoxin Contamination in Groundnut through A Combination of Genetic Resistance and Post-Harvest Management Practices. Toxins. 2019; 11 (6):315.

Chicago/Turabian Style

Manish K. Pandey; Rakesh Kumar; Arun K. Pandey; Pooja Soni; Sunil S. Gangurde; Hari K. Sudini; Jake C. Fountain; Boshou Liao; Haile Desmae; Patrick Okori; Xiaoping Chen; Huifang Jiang; Venugopal Mendu; Hamidou Falalou; Samuel Njoroge; James Mwololo; Baozhu Guo; Weijian Zhuang; Xingjun Wang; Xuanqiang Liang; Rajeev K. Varshney. 2019. "Mitigating Aflatoxin Contamination in Groundnut through A Combination of Genetic Resistance and Post-Harvest Management Practices." Toxins 11, no. 6: 315.

Research article
Published: 13 May 2019 in Plant Biotechnology Journal
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Bacterial wilt, caused by Ralstonia solanacearum, is a devastating disease affecting over 350 plant species. A few peanut cultivars were found to possess stable and durable bacterial wilt resistance (BWR). Genomics‐assisted breeding (GAB) can accelerate the process of developing resistant cultivars by using diagnostic markers. Here, we deployed sequencing‐based trait mapping approach, QTL‐seq, to discover genomic regions, candidate genes and diagnostic markers for BWR in a recombination inbred line (RIL) population (195 progenies) of peanut. The QTL‐seq analysis identified one candidate genomic region on chromosome B02 significantly associated with BWR. Mapping of newly developed single nucleotide polymorphism (SNP) markers narrowed down the region to 2.07 Mb and confirmed its major effects and stable expressions across three environments. This candidate genomic region had 49 non‐synonymous SNPs affecting 19 putative candidate genes including seven putative resistance genes (R‐genes). Two diagnostic markers were successfully validated in diverse breeding lines and cultivars, and could be deployed in genomics‐assisted breeding of varieties with enhanced BWR. This article is protected by copyright. All rights reserved.

ACS Style

Huaiyong Luo; Manish K. Pandey; Aamir W. Khan; Bei Wu; Jianbin Guo; Xiaoping Ren; Xiaojing Zhou; Yuning Chen; Weigang Chen; Li Huang; Nian Liu; Yong Lei; Boshou Liao; Rajeev K. Varshney; Huifang Jiang. Next‐generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut ( Arachis hypogaea L.). Plant Biotechnology Journal 2019, 17, 2356 -2369.

AMA Style

Huaiyong Luo, Manish K. Pandey, Aamir W. Khan, Bei Wu, Jianbin Guo, Xiaoping Ren, Xiaojing Zhou, Yuning Chen, Weigang Chen, Li Huang, Nian Liu, Yong Lei, Boshou Liao, Rajeev K. Varshney, Huifang Jiang. Next‐generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut ( Arachis hypogaea L.). Plant Biotechnology Journal. 2019; 17 (12):2356-2369.

Chicago/Turabian Style

Huaiyong Luo; Manish K. Pandey; Aamir W. Khan; Bei Wu; Jianbin Guo; Xiaoping Ren; Xiaojing Zhou; Yuning Chen; Weigang Chen; Li Huang; Nian Liu; Yong Lei; Boshou Liao; Rajeev K. Varshney; Huifang Jiang. 2019. "Next‐generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut ( Arachis hypogaea L.)." Plant Biotechnology Journal 17, no. 12: 2356-2369.

Journal article
Published: 12 March 2019 in BMC Genetics
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Aflatoxin contamination caused by Aspergillus flavus is a major constraint to peanut industry worldwide due to its toxicological effects to human and animals. Developing peanut varieties with resistance to seed infection and/or aflatoxin accumulation is the most effective and economic strategy for reducing aflatoxin risk in food chain. Breeding for resistance to aflatoxin in peanut is a challenging task for breeders because the genetic basis is still poorly understood. To identify the quantitative trait loci (QTLs) for resistance to aflatoxin contamination in peanut, a recombinant inbred line (RIL) population was developed from crossing Zhonghua 10 (susceptible) with ICG 12625 (resistant). The percent seed infection index (PSII), the contents of aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) of RILs were evaluated by a laboratory kernel inoculation assay. Two QTLs were identified for PSII including one major QTL with 11.32–13.00% phenotypic variance explained (PVE). A total of 12 QTLs for aflatoxin accumulation were detected by unconditional analysis, and four of them (qAFB1A07 and qAFB1B06.1 for AFB1, qAFB2A07 and qAFB2B06 for AFB2) exhibited major and stable effects across multiple environments with 9.32–21.02% PVE. Furthermore, not only qAFB1A07 and qAFB2A07 were co-localized in the same genetic interval on LG A07, but qAFB1B06.1 was also co-localized with qAFB2B06 on LG B06. Conditional QTL mapping also confirmed that there was a strong interaction between resistance to AFB1 and AFB2 accumulation. Genotyping of RILs revealed that qAFB1A07 and qAFB1B06.1 interacted additively to improve the resistance to both AFB1 and AFB2 accumulation. Additionally, validation of the two markers was performed in diversified germplasm collection and four accessions with resistance to aflatoxin accumulation were identified. Single major QTL for resistance to PSII and two important co-localized intervals associated with major QTLs for resistance to AFB1 and AFB2. Combination of these intervals could improve the resistance to aflatoxin accumulation in peanut. SSR markers linked to these intervals were identified and validated. The identified QTLs and associated markers exhibit potential to be applied in improvement of resistance to aflatoxin contamination.

ACS Style

Bolun Yu; Dongxin Huai; Li Huang; Yanping Kang; Xiaoping Ren; Yuning Chen; Xiaojing Zhou; Huaiyong Luo; Nian Liu; Weigang Chen; Yong Lei; Manish K. Pandey; Hari Sudini; Rajeev K. Varshney; Boshou Liao; Huifang Jiang. Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.). BMC Genetics 2019, 20, 1 -13.

AMA Style

Bolun Yu, Dongxin Huai, Li Huang, Yanping Kang, Xiaoping Ren, Yuning Chen, Xiaojing Zhou, Huaiyong Luo, Nian Liu, Weigang Chen, Yong Lei, Manish K. Pandey, Hari Sudini, Rajeev K. Varshney, Boshou Liao, Huifang Jiang. Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.). BMC Genetics. 2019; 20 (1):1-13.

Chicago/Turabian Style

Bolun Yu; Dongxin Huai; Li Huang; Yanping Kang; Xiaoping Ren; Yuning Chen; Xiaojing Zhou; Huaiyong Luo; Nian Liu; Weigang Chen; Yong Lei; Manish K. Pandey; Hari Sudini; Rajeev K. Varshney; Boshou Liao; Huifang Jiang. 2019. "Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.)." BMC Genetics 20, no. 1: 1-13.

Article
Published: 08 February 2019 in Molecular Breeding
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Peanut is an important source of edible vegetable oils worldwide. Saturated fatty acid content is a key factor that affects the quality of peanut oil; thus, reducing its content is a key objective in peanut breeding. In this study, we constructed a dense genetic map of recombinant inbred line (RIL) population (Zhonghua 10 × ICG 12625) with 1443 SSR loci, covering a total length of 2279.10 cM. Using phenotypic data from three environments, we have identified 59 additive QTLs including eight stable ones and nine epistatic QTLs for various fatty acids. Combination of conditional and unconditional QTL analyses further revealed that there was a high genetic correlation between stearic acid and very long-chain saturated fatty acids. In addition, four QTL clusters (CLB04-1, CLB04-2, CLB04-3, and CLB06) harboring major and stable QTLs for saturated fatty acids were identified, which explained 10.77–36.73%, 35.10–41.89%, 10.79–39.18%, and 4.85–20.32% phenotypic variations, respectively. The physical interval of four QTL clusters was located at pseudomolecule B04 and B06 of Arachis ipaensis, containing putative genes that encode enzymes and transcription factors involved in fatty acid biosynthesis pathways. This study comprehensively analyzed the genetic components that controlled saturated fatty acid profiles and identified four QTL clusters containing stable QTLs with large effects. Our results could provide a platform for further gene discovery and guide the development of markers for genome-wide assisted selection of varieties with desired components of saturated fatty acids.

ACS Style

Nian Liu; Hao Chen; Dongxin Huai; Fujian Xia; Li Huang; Weigang Chen; Bei Wu; Xiaoping Ren; Huaiyong Luo; Xiaojing Zhou; Yuning Chen; Yong Lei; Boshou Liao; Huifang Jiang. Four QTL clusters containing major and stable QTLs for saturated fatty acid contents in a dense genetic map of cultivated peanut (Arachis hypogaea L.). Molecular Breeding 2019, 39, 23 .

AMA Style

Nian Liu, Hao Chen, Dongxin Huai, Fujian Xia, Li Huang, Weigang Chen, Bei Wu, Xiaoping Ren, Huaiyong Luo, Xiaojing Zhou, Yuning Chen, Yong Lei, Boshou Liao, Huifang Jiang. Four QTL clusters containing major and stable QTLs for saturated fatty acid contents in a dense genetic map of cultivated peanut (Arachis hypogaea L.). Molecular Breeding. 2019; 39 (2):23.

Chicago/Turabian Style

Nian Liu; Hao Chen; Dongxin Huai; Fujian Xia; Li Huang; Weigang Chen; Bei Wu; Xiaoping Ren; Huaiyong Luo; Xiaojing Zhou; Yuning Chen; Yong Lei; Boshou Liao; Huifang Jiang. 2019. "Four QTL clusters containing major and stable QTLs for saturated fatty acid contents in a dense genetic map of cultivated peanut (Arachis hypogaea L.)." Molecular Breeding 39, no. 2: 23.

Journal article
Published: 16 January 2019 in BMC Genomics
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Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in peanut are lacking in spite of the availability of the peanut genome sequence. In this study, we identified 50 and 45 bZIP genes from Arachis duranensis and A. ipaensis genomes, respectively. Phylogenetic analysis showed that Arachis bZIP genes were classified into nine groups, and these clusters were supported by several group-specific features, including exon/intron structure, intron phases, MEME motifs, and predicted binding site structure. We also identified possible variations in DNA-binding-site specificity and dimerization properties among different Arachis bZIPs by inspecting the amino acid residues at some key sites. Our analysis of the evolutionary history analysis indicated that segmental duplication, rather than tandem duplication, contributed greatly to the expansion of this gene family, and that most Arachis bZIPs underwent strong purifying selection. Through RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, the co-expressed, differentially expressed and several well-studied homologous bZIPs were identified during seed development stages in peanut. We also used qRT-PCR to explore changes in bZIP gene expression in response to salt-treatment, and many candidate bZIPs in groups A, B, and S were proven to be associated with the salt-stress response. This study have conducted a genome-wide identification, characterization and expression analysis of bZIP genes in Arachis genomes. Our results provide insights into the evolutionary history of the bZIP gene family in peanut and the funcntion of Arachis bZIP genes during seed development and in response to salt stress. The online version of this article (10.1186/s12864-019-5434-6) contains supplementary material, which is available to authorized users.

ACS Style

Zhihui Wang; Liying Yan; Liyun Wan; Dongxin Huai; Yanping Kang; Lei Shi; Huifang Jiang; Yong Lei; Boshou Liao. Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut. BMC Genomics 2019, 20, 51 .

AMA Style

Zhihui Wang, Liying Yan, Liyun Wan, Dongxin Huai, Yanping Kang, Lei Shi, Huifang Jiang, Yong Lei, Boshou Liao. Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut. BMC Genomics. 2019; 20 (1):51.

Chicago/Turabian Style

Zhihui Wang; Liying Yan; Liyun Wan; Dongxin Huai; Yanping Kang; Lei Shi; Huifang Jiang; Yong Lei; Boshou Liao. 2019. "Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut." BMC Genomics 20, no. 1: 51.

Journal article
Published: 06 January 2019 in The Crop Journal
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The inheritance of pod- and seed-number traits (PSNT) in peanut (Arachis hypogaea L.) is poorly understood. In the present study, a recombinant inbred line (RIL) population of 188 lines was used to map quantitative trait loci (QTL) for number of seeds per pod (NSP), number of pods per plant (NPP), and numbers of one-, two-, and three-seeded pods per plant (N1PP, N2PP, and N3PP) in four environments. A total of 28 consensus QTL and 14 single QTL were identified, including 11 major and stable QTL. Four major and stable QTL including qN3PPA5.2, qN3PPA5.4, qN3PPA5.5, and qN3PPA5.7 each explained 12.3%–33.0% of phenotype variation. By use of another integrated linkage map for the A5 group (hereafter referred to as INT A5 group), QTL for PSNT were located in seven intervals of 0.73–9.68 Mb in length on chromosome A05, and candidate genes underlying N3PP were suggested. These findings shed light on the genetic basis of PSNT. Major QTL for N3PP could be used as candidates for further positional cloning.

ACS Style

Yuning Chen; Zhihui Wang; Xiaoping Ren; Li Huang; Jianbin Guo; Jiaojiao Zhao; Xiaojing Zhou; Liying Yan; Huaiyong Luo; Nian Liu; Weigang Chen; Liyun Wan; Yong Lei; Boshou Liao; Dongxin Huai; Huifang Jiang. Identification of major QTL for seed number per pod on chromosome A05 of tetraploid peanut (Arachis hypogaea L.). The Crop Journal 2019, 7, 238 -248.

AMA Style

Yuning Chen, Zhihui Wang, Xiaoping Ren, Li Huang, Jianbin Guo, Jiaojiao Zhao, Xiaojing Zhou, Liying Yan, Huaiyong Luo, Nian Liu, Weigang Chen, Liyun Wan, Yong Lei, Boshou Liao, Dongxin Huai, Huifang Jiang. Identification of major QTL for seed number per pod on chromosome A05 of tetraploid peanut (Arachis hypogaea L.). The Crop Journal. 2019; 7 (2):238-248.

Chicago/Turabian Style

Yuning Chen; Zhihui Wang; Xiaoping Ren; Li Huang; Jianbin Guo; Jiaojiao Zhao; Xiaojing Zhou; Liying Yan; Huaiyong Luo; Nian Liu; Weigang Chen; Liyun Wan; Yong Lei; Boshou Liao; Dongxin Huai; Huifang Jiang. 2019. "Identification of major QTL for seed number per pod on chromosome A05 of tetraploid peanut (Arachis hypogaea L.)." The Crop Journal 7, no. 2: 238-248.

Research article
Published: 13 December 2018 in Plant Biotechnology Journal
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Cultivated peanut (Arachis hypogaea L.) is an important grain legume providing high‐quality cooking oil, rich proteins and other nutrients. Shelling percentage (SP) is the 2nd most important agronomic trait after pod yield and this trait significantly affects the economic value of peanut in the market. Deployment of diagnostic markers through genomics‐assisted breeding (GAB) can accelerate the process of developing improved varieties with enhanced SP. In this context, we deployed the QTL‐seq approach to identify genomic regions and candidate genes controlling SP in a recombinant inbred line population (Yuanza 9102 × Xuzhou 68‐4). Four libraries (two parents and two extreme bulks) were constructed and sequenced, generating 456.89–790.32 million reads and achieving 91.85%–93.18% genome coverage and 14.04–21.37 mean read depth. Comprehensive analysis of two sets of data (Yuanza 9102/two bulks and Xuzhou 68‐4/two bulks) using the QTL‐seq pipeline resulted in discovery of two overlapped genomic regions (2.75Mb on A09 and 1.1Mb on B02). Nine candidate genes affected by ten SNPs with nonsynonymous effects or in UTRs were identified in these regions for SP. Cost‐effective KASP (Kompetitive Allele Specific PCR) markers were developed for one SNP from A09 and three SNPs from B02 chromosome. Genotyping of the mapping population with these newly developed KASP markers confirmed the major control and stable expressions of these genomic regions across five environments. The identified candidate genomic regions and genes for SP further provide opportunity for gene cloning and deployment of diagnostic markers in molecular breeding for achieving high SP in improved varieties. This article is protected by copyright. All rights reserved.

ACS Style

Huaiyong Luo; Manish K. Pandey; Aamir W Khan; Jianbin Guo; Bei Wu; Yan Cai; Li Huang; Xiaojing Zhou; Yuning Chen; Weigang Chen; Nian Liu; Yong Lei; Boshou Liao; Rajeev K. Varshney; Huifang Jiang. Discovery of genomic regions and candidate genes controlling shelling percentage using QTL ‐seq approach in cultivated peanut ( Arachis hypogaea L.). Plant Biotechnology Journal 2018, 17, 1248 -1260.

AMA Style

Huaiyong Luo, Manish K. Pandey, Aamir W Khan, Jianbin Guo, Bei Wu, Yan Cai, Li Huang, Xiaojing Zhou, Yuning Chen, Weigang Chen, Nian Liu, Yong Lei, Boshou Liao, Rajeev K. Varshney, Huifang Jiang. Discovery of genomic regions and candidate genes controlling shelling percentage using QTL ‐seq approach in cultivated peanut ( Arachis hypogaea L.). Plant Biotechnology Journal. 2018; 17 (7):1248-1260.

Chicago/Turabian Style

Huaiyong Luo; Manish K. Pandey; Aamir W Khan; Jianbin Guo; Bei Wu; Yan Cai; Li Huang; Xiaojing Zhou; Yuning Chen; Weigang Chen; Nian Liu; Yong Lei; Boshou Liao; Rajeev K. Varshney; Huifang Jiang. 2018. "Discovery of genomic regions and candidate genes controlling shelling percentage using QTL ‐seq approach in cultivated peanut ( Arachis hypogaea L.)." Plant Biotechnology Journal 17, no. 7: 1248-1260.

Original article
Published: 20 October 2017 in Theoretical and Applied Genetics
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Co-localized intervals and candidate genes were identified for major and stable QTLs controlling pod weight and size on chromosomes A07 and A05 in an RIL population across four environments. Cultivated peanut (Arachis hypogaea L.) is an important legume crops grown in > 100 countries. Hundred-pod weight (HPW) is an important yield trait in peanut, but its underlying genetic mechanism was not well studied. In this study, a mapping population (Xuhua 13 × Zhonghua 6) with 187 recombinant inbred lines (RILs) was developed to map quantitative trait loci (QTLs) for HPW together with pod length (PL) and pod width (PW) by both unconditional and conditional QTL analyses. A genetic map covering 1756.48 cM was constructed with 817 markers. Additive effects, epistatic interactions, and genotype-by-environment interactions were analyzed using the phenotyping data generated across four environments. Twelve additive QTLs were identified on chromosomes A05, A07, and A08 by unconditional analysis, and five of them (qPLA07, qPLA05.1, qPWA07, qHPWA07.1, and qHPWA05.2) showed major and stable expressions in all environments. Conditional QTL mapping found that PL had stronger influences on HPW than PW. Notably, qHPWA07.1, qPLA07, and qPWA07 that explained 17.93–43.63% of the phenotypic variations of the three traits were co-localized in a 5 cM interval (1.48 Mb in physical map) on chromosome A07 with 147 candidate genes related to catalytic activity and metabolic process. In addition, qHPWA05.2 and qPLA05.1 were co-localized with minor QTL qPWA05.2 to a 1.3 cM genetic interval (280 kb in physical map) on chromosome A05 with 12 candidate genes. This study provides a comprehensive characterization of the genetic components controlling pod weight and size as well as candidate QTLs and genes for improving pod yield in future peanut breeding.

ACS Style

Huaiyong Luo; Boshou Liao; Huifang Jiang; Jianbin Guo; Xiaoping Ren; Weigang Chen; Li Huang; Xiaojing Zhou; Yuning Chen; Nian Liu; Fei Xiong; Yong Lei. Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (Arachis hypogaea L.). Theoretical and Applied Genetics 2017, 131, 267 -282.

AMA Style

Huaiyong Luo, Boshou Liao, Huifang Jiang, Jianbin Guo, Xiaoping Ren, Weigang Chen, Li Huang, Xiaojing Zhou, Yuning Chen, Nian Liu, Fei Xiong, Yong Lei. Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (Arachis hypogaea L.). Theoretical and Applied Genetics. 2017; 131 (2):267-282.

Chicago/Turabian Style

Huaiyong Luo; Boshou Liao; Huifang Jiang; Jianbin Guo; Xiaoping Ren; Weigang Chen; Li Huang; Xiaojing Zhou; Yuning Chen; Nian Liu; Fei Xiong; Yong Lei. 2017. "Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (Arachis hypogaea L.)." Theoretical and Applied Genetics 131, no. 2: 267-282.