Cultivated peanut, or groundnut (Arachis hypogaea L.), is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). In recent years, many efforts have been made to construct linkage maps in cultivated peanut, but almost all of these maps were constructed using low-throughput molecular markers, and most show a low density, directly influencing the value of their applications. With advances in next-generation sequencing (NGS) technology, the construction of high-density genetic maps has become more achievable in a cost-effective and rapid manner. The objective of this study was to establish a high-density single nucleotide polymorphism (SNP)-based genetic map for cultivated peanut by analyzing next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq) reads. We constructed reduced representation libraries (RRLs) for two A. hypogaea lines and 166 of their recombinant inbred line (RIL) progenies using the ddRADseq technique. Approximately 175 gigabases of data containing 952,679,665 paired-end reads were obtained following Solexa sequencing. Mining this dataset, 53,257 SNPs were detected between the parents, of which 14,663 SNPs were also detected in the population, and 1,765 of the obtained polymorphic markers met the requirements for use in the construction of a genetic map. Among 50 randomly selected in silico SNPs, 47 were able to be successfully validated. One linkage map was constructed, which was comprised of 1,685 marker loci, including 1,621 SNPs and 64 simple sequence repeat (SSR) markers. The map displayed a distribution of the markers into 20 linkage groups (LGs A01–A10 and B01–B10), spanning a distance of 1,446.7 cM. The alignment of the LGs from this map was shown in comparison with a previously integrated consensus map from peanut. This study showed that the ddRAD library combined with NGS allowed the rapid discovery of a large number of SNPs in the cultivated peanut. The first high density SNP-based linkage map for A. hypogaea was generated that can serve as a reference map for cultivated Arachis species and will be useful in genetic mapping. Our results contribute to the available molecular marker resources and to the assembly of a reference genome sequence for the peanut.

Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be diverse transcriptional regulators, playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. In this study, we identified 428 bZIP genes encoding 585 distinct proteins in six legumes, Glycine max, Medicago truncatula, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Lotus japonicus. The legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. Four kinds of intron patterns (a–d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. We predicted the DNA-binding patterns and the dimerization properties, based on the characteristic features in the basic and hinge regions and the Leu zipper, respectively, which indicated that some highly conserved amino acid residues existed across each major group. The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. We also detected several key legume bZIP genes involved in drought- and salt-responses by comparing fold changes of expression values in drought-stressed or salt-stressed roots and leaves. In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses.

Background: Stem rot caused by Sclerotium rolfsii is a very important soil-borne disease of peanut. S. rolfsii is a necrotrophic plant pathogenic fungus with an extensive host range and worldwide distribution. It can infect peanut stems, roots, pegs and pods, leading to varied yield losses. S. rolfsii strains GP3 and ZY collected from peanut in different provinces of China exhibited a significant difference in aggressiveness on peanut plants by artificial inoculation test. In this study, de-novo genome sequencing of these two distinct strains was performed aiming to reveal the genomic basis of difference in aggressiveness. Results: Scleotium rolfsii strains GP3 and ZY, with weak and high aggressiveness on peanut plants, exhibited similar growth rate and oxalic acid production in laboratory. The genomes of S. rolfsii strains GP3 and ZY were sequenced by Pacbio long read technology and exhibited 70.51 Mb and 70.61 Mb, with contigs of 27 and 23, and encoded 17,097 and 16,743 gene models, respectively. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires, which might be associated with aggressiveness, differed between GP3 and ZY. There were 58 and 45 unique pathogen-host interaction (PHI) genes in GP3 and ZY, respectively. The ZY strain had more carbohydrate-active enzymes (CAZymes) in its secretome than GP3, especially in the glycoside hydrolase family (GH), the carbohydrate esterase family (CBM), and the polysaccharide lyase family (PL). GP3 and ZY also had different effector candidates and putative secondary metabolite synthetic gene clusters. These results indicated that differences in PHI, secreted CAZymes, effectors and secondary metabolites may play important roles in aggressive difference between these two strains. Conclusions: The data provided a further understanding of the S. rolfsii genome. Genomic comparison provided clues to the difference in aggressiveness of S. rolfsii strains.

The cultivated peanut (Arachis hypogaea L.) is an important oil and food crop in the world. Pod- and kernel-related traits are direct factors involved in determining the yield of the peanut. However, the genetic basis underlying pod- and kernel-related traits in the peanut remained largely unknown, which hampered the improvement of peanut through marker-assisted selection. To understand the genetic basis underlying pod- and kernel-related traits in the peanut and provide more useful information for marker-assisted breeding, we conducted quantitative trait locus (QTL) analysis for pod length and width and seed length and width by use of two F2:3 populations derived from cultivar Fuchuan Dahuasheng × ICG 6375 (FI population) and cultivar Xuhua 13 × cultivar Zhonghua 6 (XZ population) in this study. Two genetic maps containing 347 and 228 polymorphic markers were constructed for FI and XZ populations respectively. In total, 39 QTLs explaining 1.25–26.11 % of the phenotypic variations were detected in two populations. For the FI population, 26 QTLs were detected between the two environments, among which twelve were not mapped before. For the XZ population, thirteen QTLs were detected, among which eight were not reported before. One QTL for pod width was repeatedly mapped between the two populations. The QTL analyses for pod length and width and seed length and width were conducted in this study using two mapping populations. Novel QTLs were identified, which included two for pod length, four for pod width, five for seed length and one for seed width in the FI population, and three for pod length, three for pod width and two for seed width in the XZ population. Our results will be helpful for improving pod- and seed-related traits in peanuts through marker-assisted selection.

Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs), Eastern Asia (EAs), and Western Africa (WAf) were highly diversified, while those from Western Asia (WAs), Northern Africa (NAf), and Southeastern Africa (SAf) had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions.

One hundred and forty-six highly polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 196 peanut (Arachis Hypogaea L.) cultivars which had been extensively planted in different regions in China. These SSR markers amplified 440 polymorphic bands with an average of 2.99, and the average gene diversity index was 0.11. Eighty-six rare alleles with a frequency of less than 1% were identified in these cultivars. The largest Fst or genetic distance was found between the cultivars that adapted to the south regions and those to the north regions in China. A neighbor-joining tree of cultivars adapted to different ecological regions was constructed based on pairwise Nei’s genetic distances, which showed a significant difference between cultivars from the south and the north regions. A model-based population structure analysis divided these peanut cultivars into five subpopulations (P1a, P1b, P2, P3a and P3b). P1a and P1b included most the cultivars from the southern provinces including Guangdong, Guangxi and Fujian. P2 population consisted of the cultivars from Hubei province and parts from Shandong and Henan. P3a and P3b had cultivars from the northern provinces including Shandong, Anhui, Henan, Hebei, Jiangsu and the Yangtze River region including Sichuan province. The cluster analysis, PCoA and PCA based on the marker genotypes, revealed five distinct clusters for the entire population that were related to their germplasm regions. The results indicated that there were obvious genetic variations between cultivars from the south and the north, and there were distinct genetic differentiation among individual cultivars from the south and the north. Taken together, these results provided a molecular basis for understanding genetic diversity of Chinese peanut cultivars.