This page has only limited features, please log in for full access.
Fruit and seed size are important yield component traits that have been selected during crop domestication. In previous studies, Advanced Backcross Quantitative Trait Loci (AB-QTL) and Chromosome Segment Substitution Line (CSSL) populations were developed in peanut by crossing the cultivated variety Fleur11 and a synthetic wild allotetraploid (Arachis. ipaensis × Arachis. duranensis)4x. In the AB-QTL population, a major QTL for pod and seed size was detected in a ~5 Mb interval in the proximal region of chromosome A07. In the CSSL population, the line 12CS_091, which carries the QTL region and that produces smaller pods and seeds than Fleur11, was identified. In this study, we used a two-step strategy to fine-map the seed size QTL region on chromosome A07. We developed new SSR and SNP markers, as well as near-isogenic lines (NILs) in the target QTL region. We first located the QTL in ~1 Mb region between two SSR markers, thanks to the genotyping of a large F2 population of 2172 individuals and a single marker analysis approach. We then used nine new SNP markers evenly distributed in the refined QTL region to genotype 490 F3 plants derived from 88 F2, and we selected 10 NILs. The phenotyping of the NILs and marker/trait association allowed us to narrowing down the QTL region to a 168.37 kb chromosome segment, between the SNPs Aradu_A07_1148327 and Aradu_A07_1316694. This region contains 22 predicted genes. Among these genes, Aradu.DN3DB and Aradu.RLZ61, which encode a transcriptional regulator STERILE APETALA-like (SAP) and an F-box SNEEZY (SNE), respectively, were of particular interest. The function of these genes in regulating the variation of fruit and seed size is discussed. This study will contribute to a better knowledge of genes that have been targeted during peanut domestication.
Mounirou Hachim Alyr; Justine Pallu; Aissatou Sambou; Joel Romaric Nguepjop; Maguette Seye; Hodo-Abalo Tossim; Yvette Rachelle Djiboune; Djibril Sane; Jean-François Rami; Daniel Fonceka. Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.). Genes 2020, 11, 1402 .
AMA StyleMounirou Hachim Alyr, Justine Pallu, Aissatou Sambou, Joel Romaric Nguepjop, Maguette Seye, Hodo-Abalo Tossim, Yvette Rachelle Djiboune, Djibril Sane, Jean-François Rami, Daniel Fonceka. Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.). Genes. 2020; 11 (12):1402.
Chicago/Turabian StyleMounirou Hachim Alyr; Justine Pallu; Aissatou Sambou; Joel Romaric Nguepjop; Maguette Seye; Hodo-Abalo Tossim; Yvette Rachelle Djiboune; Djibril Sane; Jean-François Rami; Daniel Fonceka. 2020. "Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.)." Genes 11, no. 12: 1402.
Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolorL. Moench) in West Africa has diversified across a mosaic of cultures and end-uses, and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing was used to generate 159,101 high-quality biallelic SNPs, with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = 0.00045), only slightly less than in a global diversity panel (π = 0.00055). Linkage disequilibrium decayed to background level (r 2 < 0.1) by ~50 kb in the WASAP. Genome-wide diversity was structured both by botanical type, and by populations within botanical type, with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies of days to flowering and plant height revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height lociDw3andSbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in US germplasm (Ma6andSbCN8) suggests that photoperiodic flowering in WA sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in West Africa.
Jacques M. Faye; Fanna Maina; Eyanawa A. Akata; Bassirou Sine; Cyril Diatta; Aissata Mamadou; Sandeep R Marla; Sophie Bouchet; Niaba Teme; Jean-Francois Rami; Daniel Fonceka; Ndiaga Cisse; Geoffrey P. Morris. A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum. 2020, 1 .
AMA StyleJacques M. Faye, Fanna Maina, Eyanawa A. Akata, Bassirou Sine, Cyril Diatta, Aissata Mamadou, Sandeep R Marla, Sophie Bouchet, Niaba Teme, Jean-Francois Rami, Daniel Fonceka, Ndiaga Cisse, Geoffrey P. Morris. A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum. . 2020; ():1.
Chicago/Turabian StyleJacques M. Faye; Fanna Maina; Eyanawa A. Akata; Bassirou Sine; Cyril Diatta; Aissata Mamadou; Sandeep R Marla; Sophie Bouchet; Niaba Teme; Jean-Francois Rami; Daniel Fonceka; Ndiaga Cisse; Geoffrey P. Morris. 2020. "A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum." , no. : 1.
Cultivated peanut is an allotetraploid (2n = 4× = 40) with narrow genetic diversity. In previous studies, we developed an advanced backcross quantitative trait loci (AB-QTL) population from the cross between the synthetic allotetraploid ((Arachis ipaensis × Arachis duranensis)4×) and the cultivated variety Fleur11, and mapped several quantitative trait loci (QTLs) involved in yield and yield components. We also developed a chromosome segment substitution line (CSSL) population as a way to mendelize the QTLs and analyzing their effects. In this study, 16 CSSLs were used for assessing the contribution of wild alleles in yield performance and stability across environments, as well as validating QTLs for pod and seed size. The CSSLs and the recurrent parent Fleur11, used as a check, were assessed using an alpha lattice design in three locations during two consecutive rainy seasons in Senegal, totaling six environments. Our results showed that the chromosome segments from the wild species, in general, have no yield disadvantage and contributed positive variation to yield-related traits. Most of the QTLs detected for pod and seed size in the AB-QTL on linkage groups A07, A08, A09, and B06 were also found in the CSSLs, showing that the CSSLs used in this study are accurate material for QTL validation. Several new QTLs have also been identified. Two CSSLs (12CS_031 and 12CS_069) showed consistently higher pod and seed size than Fleur11 in all environments, suggesting that the QTLs were consistent and stable. Our study opens the way for pyramiding these QTLs for peanut improvement.
Hodo-Abalo Tossim; Joel Romaric Nguepjop; Cyril Diatta; Aissatou Sambou; Maguette Seye; Djibril Sane; Jean-François Rami; Daniel Fonceka. Assessment of 16 Peanut (Arachis hypogaea L.) CSSLs Derived from an Interspecific Cross for Yield and Yield Component Traits: QTL Validation. Agronomy 2020, 10, 583 .
AMA StyleHodo-Abalo Tossim, Joel Romaric Nguepjop, Cyril Diatta, Aissatou Sambou, Maguette Seye, Djibril Sane, Jean-François Rami, Daniel Fonceka. Assessment of 16 Peanut (Arachis hypogaea L.) CSSLs Derived from an Interspecific Cross for Yield and Yield Component Traits: QTL Validation. Agronomy. 2020; 10 (4):583.
Chicago/Turabian StyleHodo-Abalo Tossim; Joel Romaric Nguepjop; Cyril Diatta; Aissatou Sambou; Maguette Seye; Djibril Sane; Jean-François Rami; Daniel Fonceka. 2020. "Assessment of 16 Peanut (Arachis hypogaea L.) CSSLs Derived from an Interspecific Cross for Yield and Yield Component Traits: QTL Validation." Agronomy 10, no. 4: 583.
Peanut aflatoxin contamination caused by Aspergillus flavus is a serious constraint for food safety and human health in Senegal. The present study aimed to identify sources of resistance for A. flavus colonization and aflatoxin contamination. Thus, seeds from 67 peanut genotypes were tested under laboratory conditions. Aqueous conidial suspension of an aflatoxinogenic strain of A. flavus was used for inoculation in Petri dishes containing ten seeds of each genotype, and data on incidence and severity were recorded. Total aflatoxin concentration in seeds was determined on 15th day after inoculation using mReader® method. Results showed a significant (p<0.001) variation of aflatoxin, incidence and severity among the tested peanut genotypes. Incidence ranged from 0 to 70% with a mean of 20.36 ± 0.8%. Out of the 67 genotypes, eight showed incidence less than 10%. Severity ranged from 0 to 44% with a mean value of 8.82 ± 0.45%. The genotype 12CS_104 showed aflatoxin concentration level in conformity with the European standard (4 ppb). Out of three clusters revealed by hierarchical classification based on disease incidence and severity, the cluster 1 contained 33 genotypes characterised by low incidence and severity values. These genotypes can be tested under field conditions to confirm their resistance to A flavus.
Richard Moïse Alansou Dieme; Issa Faye; Yedomon Ange Bovys Zoclanclounon; Daniel Fonceka; Ousmane Ndoye; Papa Madiallacke Diedhiou. Identification of Sources of Resistance for Peanut Aspergillus flavus Colonization and Aflatoxin Contamination. International Journal of Agronomy 2018, 2018, 1 -7.
AMA StyleRichard Moïse Alansou Dieme, Issa Faye, Yedomon Ange Bovys Zoclanclounon, Daniel Fonceka, Ousmane Ndoye, Papa Madiallacke Diedhiou. Identification of Sources of Resistance for Peanut Aspergillus flavus Colonization and Aflatoxin Contamination. International Journal of Agronomy. 2018; 2018 ():1-7.
Chicago/Turabian StyleRichard Moïse Alansou Dieme; Issa Faye; Yedomon Ange Bovys Zoclanclounon; Daniel Fonceka; Ousmane Ndoye; Papa Madiallacke Diedhiou. 2018. "Identification of Sources of Resistance for Peanut Aspergillus flavus Colonization and Aflatoxin Contamination." International Journal of Agronomy 2018, no. : 1-7.
Pearl millet plays a major role in food security in arid and semi-arid areas of Africa and India. However, it lags behind the other cereal crops in terms of genetic improvement. The recent sequencing of its genome opens the way to the use of modern genomic tools for breeding. Our study aimed at identifying genetic components involved in early drought stress tolerance as a first step toward the development of improved pearl millet varieties or hybrids. A panel of 188 inbred lines from West Africa was phenotyped under early drought stress and well-irrigated conditions. We found a strong impact of drought stress on yield components. This impact was variable between inbred lines. We then performed an association analysis with a total of 392,493 SNPs identified using Genotyping-by-Sequencing (GBS). Correcting for genetic relatedness, genome wide association study identified QTLs for biomass production in early drought stress conditions and for stay-green trait. In particular, genes involved in the sirohaem and wax biosynthesis pathways were found to co-locate with association loci. Our results open the way to use genomic selection to breed pearl millet lines with improved yield under drought stress.
Marilyne Debieu; Bassirou Sine; Sixtine Passot; Alexandre Grondin; Ae Akata; Prakash Gangashetty; Vincent Vadez; Pascal Gantet; Daniel Fonceka; Laurent Cournac; Charles Tom Hash; Na Kane; Yves Vigouroux; Laurent Laplaze; Eyanawa Akata; Ndjido Kane. Response to early drought stress and identification of QTLs controlling biomass production under drought in pearl millet. 2018, 373233 .
AMA StyleMarilyne Debieu, Bassirou Sine, Sixtine Passot, Alexandre Grondin, Ae Akata, Prakash Gangashetty, Vincent Vadez, Pascal Gantet, Daniel Fonceka, Laurent Cournac, Charles Tom Hash, Na Kane, Yves Vigouroux, Laurent Laplaze, Eyanawa Akata, Ndjido Kane. Response to early drought stress and identification of QTLs controlling biomass production under drought in pearl millet. . 2018; ():373233.
Chicago/Turabian StyleMarilyne Debieu; Bassirou Sine; Sixtine Passot; Alexandre Grondin; Ae Akata; Prakash Gangashetty; Vincent Vadez; Pascal Gantet; Daniel Fonceka; Laurent Cournac; Charles Tom Hash; Na Kane; Yves Vigouroux; Laurent Laplaze; Eyanawa Akata; Ndjido Kane. 2018. "Response to early drought stress and identification of QTLs controlling biomass production under drought in pearl millet." , no. : 373233.
Cultivated peanut and synthetics are allotetraploids (2n=4x=40) with two homeologous sets of chromosomes. Meiosis in allotetraploid peanut is generally thought to show diploid-like behavior. However, a recent study pointed out the occurrence of recombination between homeologous chromosomes, especially when synthetic allotetraploids are used, challenging the view of disomic inheritance in peanut. In this study, we investigated the meiotic behavior of allotetraploid peanut using 380 SSR markers and 90 F2 progeny derived from the cross between Arachis hypogaea cv Fleur 11 (AABB) and ISATGR278-18 (AAKK), a synthetic allotetraploid that harbors a K-genome that was reported to pair with the cultivated B-genome during meiosis. Segregation analysis of SSR markers showed 42 codominant SSRs with unexpected null bands among some progeny. Chi-square tests for these loci deviate from the expected 1:2:1 Mendelian ratio under disomic inheritance. A linkage map of 357 codominant loci aligned on 20 linkage groups (LGs) with a total length of 1728 cM, averaging 5.1 cM between markers, was developed. Among the ten homeologous sets of LGs, one set consisted of markers that all segregated in a polysomic-like pattern, 6 in a likely disomic pattern and the 3 remaining in a mixed pattern with disomic and polysomic loci clustered on the same LG. Moreover, we reported a substitution of homeologous chromosomes in some progeny. Our results suggest that the homeologous recombination events occurred between the A and K genomes in the newly synthesized allotetraploid and have been highlighted in the progeny. Homeologous exchanges are rarely observed in tetraploid peanut and have not yet been reported for AAKK and AABB genomes. The implications of these results on peanut breeding are discussed.
Joel R. Nguepjop; Hodo-Abalo Tossim; Joseph M. Bell; Jean-François Rami; Shivali Sharma; Brigitte Courtois; Nalini Mallikarjuna; Djibril Sane; Daniel Fonceka. Evidence of Genomic Exchanges between Homeologous Chromosomes in a Cross of Peanut with Newly Synthetized Allotetraploid Hybrids. Frontiers in Plant Science 2016, 7, 1 .
AMA StyleJoel R. Nguepjop, Hodo-Abalo Tossim, Joseph M. Bell, Jean-François Rami, Shivali Sharma, Brigitte Courtois, Nalini Mallikarjuna, Djibril Sane, Daniel Fonceka. Evidence of Genomic Exchanges between Homeologous Chromosomes in a Cross of Peanut with Newly Synthetized Allotetraploid Hybrids. Frontiers in Plant Science. 2016; 7 ():1.
Chicago/Turabian StyleJoel R. Nguepjop; Hodo-Abalo Tossim; Joseph M. Bell; Jean-François Rami; Shivali Sharma; Brigitte Courtois; Nalini Mallikarjuna; Djibril Sane; Daniel Fonceka. 2016. "Evidence of Genomic Exchanges between Homeologous Chromosomes in a Cross of Peanut with Newly Synthetized Allotetraploid Hybrids." Frontiers in Plant Science 7, no. : 1.
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.
Komivi Dossa; Xin Wei; Yanxin Zhang; Daniel Fonceka; Wenjuan Yang; Diaga Diouf; Boshou Liao; Ndiaga Cisse; Xiurong Zhang. Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation. Genes 2016, 7, 14 .
AMA StyleKomivi Dossa, Xin Wei, Yanxin Zhang, Daniel Fonceka, Wenjuan Yang, Diaga Diouf, Boshou Liao, Ndiaga Cisse, Xiurong Zhang. Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation. Genes. 2016; 7 (4):14.
Chicago/Turabian StyleKomivi Dossa; Xin Wei; Yanxin Zhang; Daniel Fonceka; Wenjuan Yang; Diaga Diouf; Boshou Liao; Ndiaga Cisse; Xiurong Zhang. 2016. "Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation." Genes 7, no. 4: 14.
Producing varieties tailored for sustainable agriculture, especially with high resilience in response to environmental constraints, is a challenge for geneticists. In the framework of climate risk characterization regarding drought, a multidisciplinary approach combining ecophysiology and genetics could be effective for developing varietal ideotypes that combine adaptive traits that could be useful for breeding. Selection initiatives geared towards obtaining varieties with high drought resistance are focused on natural or hybridization-based diversity and on adaptive trait screening tests. Examples of research programmes developed in partnership by CIRAD are presented with regard to two tropical crops—cotton and groundnut. The beneficial features of African sorghum associated with its photoperiodic nature are discussed. Broad-ranging investigations to tap the gene pool of wild species related to cultivated species are required to make effective use of the genetic diversity.
Jean-Marc Lacape; Romain Loison; Daniel Foncéka. Enhanced Drought Adaptation in African Savanna Crops. Climate Change and Agriculture Worldwide 2015, 59 -71.
AMA StyleJean-Marc Lacape, Romain Loison, Daniel Foncéka. Enhanced Drought Adaptation in African Savanna Crops. Climate Change and Agriculture Worldwide. 2015; ():59-71.
Chicago/Turabian StyleJean-Marc Lacape; Romain Loison; Daniel Foncéka. 2015. "Enhanced Drought Adaptation in African Savanna Crops." Climate Change and Agriculture Worldwide , no. : 59-71.
Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication.
Daniel Fonceka; Hodo-Abalo Tossim; Ronan Rivallan; Hélène Vignes; Issa Faye; Ousmane Ndoye; Márcio C Moretzsohn; David J Bertioli; Jean-Christophe Glaszmann; Brigitte Courtois; Jean-François Rami. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biology 2012, 12, 26 -26.
AMA StyleDaniel Fonceka, Hodo-Abalo Tossim, Ronan Rivallan, Hélène Vignes, Issa Faye, Ousmane Ndoye, Márcio C Moretzsohn, David J Bertioli, Jean-Christophe Glaszmann, Brigitte Courtois, Jean-François Rami. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biology. 2012; 12 (1):26-26.
Chicago/Turabian StyleDaniel Fonceka; Hodo-Abalo Tossim; Ronan Rivallan; Hélène Vignes; Issa Faye; Ousmane Ndoye; Márcio C Moretzsohn; David J Bertioli; Jean-Christophe Glaszmann; Brigitte Courtois; Jean-François Rami. 2012. "Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding." BMC Plant Biology 12, no. 1: 26-26.
Peanut (Arachis hypogaea L.) is widely used as a food and cash crop around the world. It is considered to be an allotetraploid (2n = 4x = 40) originated from a single hybridization event between two wild diploids. The most probable hypothesis gave A. duranensis as the wild donor of the A genome and A. ipaënsis as the wild donor of the B genome. A low level of molecular polymorphism is found in cultivated germplasm and up to date few genetic linkage maps have been published. The utilization of wild germplasm in breeding programs has received little attention due to the reproductive barriers between wild and cultivated species and to the technical difficulties encountered in making large number of crosses. We report here the development of a SSR based genetic map and the analysis of genome-wide segment introgressions into the background of a cultivated variety through the utilization of a synthetic amphidiploid between A. duranensis and A. ipaënsis.
Daniel Fonceka; Tossim Hodo-Abalo; Ronan Rivallan; Issa Faye; Mbaye Ndoye Sall; Ousmane Ndoye; Alessandra P Fávero; David J Bertioli; Jean-Christophe Glaszmann; Brigitte Courtois; Jean-François Rami. Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid. BMC Plant Biology 2009, 9, 103 -103.
AMA StyleDaniel Fonceka, Tossim Hodo-Abalo, Ronan Rivallan, Issa Faye, Mbaye Ndoye Sall, Ousmane Ndoye, Alessandra P Fávero, David J Bertioli, Jean-Christophe Glaszmann, Brigitte Courtois, Jean-François Rami. Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid. BMC Plant Biology. 2009; 9 (1):103-103.
Chicago/Turabian StyleDaniel Fonceka; Tossim Hodo-Abalo; Ronan Rivallan; Issa Faye; Mbaye Ndoye Sall; Ousmane Ndoye; Alessandra P Fávero; David J Bertioli; Jean-Christophe Glaszmann; Brigitte Courtois; Jean-François Rami. 2009. "Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid." BMC Plant Biology 9, no. 1: 103-103.