Biology subjects

Cisse, N.

Publications and source records attributed to Cisse, N..

6 recordsLinked to original sources

bioRxiv2021

Quantitative and population genomics suggest a broad role of staygreen loci in the drought adaptation of sorghum

O_LIDrought is a major constraint on plant productivity globally. Sorghum (Sorghum bicolor) landraces have evolved in drought-prone regions, but the genetics of their adaptation is not yet understood. Loci underlying stay-green post-flowering drought tolerance (Stg), have been identified in a temperate breeding line, but their role in drought adaptation of tropical sorghum is to be elucidated. C_LIO_LIWe phenotyped 590 diverse sorghum accessions from West Africa under field-based managed drought stress, pre-flowering (WS1) and post-flowering (WS2) over several years and conducted genome-wide association studies (GWAS). C_LIO_LIBroad-sense heritability for grain and biomass yield components was high (33-92%) across environments. There was a significant correlation between stress tolerance index (STI) for grain weight across WS1 and WS2. GWAS revealed that SbZfl1 and SbCN12, orthologs of maize flowering genes, likely underlie flowering time variation under these conditions. GWAS further identified associations (n = 134) for STI and drought effects on yield components, including 16 putative pleiotropic associations. Thirty of the associations colocalized with Stg1-4 loci and had large effects. Seven lead associations, including some within Stg1, overlapped with positive selection outliers. C_LIO_LIOur findings reveal natural genetic variation for drought tolerance-related traits, and suggest a broad role of Stg loci in drought adaptation of sorghum. C_LI

plant biology↗

bioRxiv2020

A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum

Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. 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 ({pi} = 0.00045), only slightly less than in a global diversity panel ({pi} = 0.00055). Linkage disequilibrium decayed to background level (r2 < 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 loci Dw3 and SbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in US germplasm (Ma6 and SbCN8) 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.

genomics↗

bioRxiv2019

Novel ankyrin-repeat mutant and modifiers of a kafirin mutant improve sorghum protein digestibility

Sorghum is a staple food for over 500 million people in Sub-Saharan Africa and Asia, however, sorghum proteins are poorly digested when wet-cooked. Three sorghum mutants were identified in a mutagenized population of the inbred line BTx623 that showed a 23-37% increase in wet-cooked protein digestibility compared to their unmutagenized parent. Furthermore, in comparison to the known high lysine, highly digestible sorghum mutant, P721Q, these mutants had 9% more protein overall that was 10% more digestible, had 12% more lysine, as well as better seed hardness. Using bulked segregant analysis based on whole genome sequencing data, we identified unique genomic regions on chromosome 5 of each EMS mutant that are associated with the increase in protein digestibility. Analyzing shared mutations in candidate genes, the high protein digestibility phenotype in one mutant is linked to a point mutation in a novel, ankyrin repeat protein. In another, the increase is associated with a mutation in a kafirin gene and suggests novel genetic modifiers. This study provides material and molecular markers that can be used to enhance sorghum nutritional value, contribute to fighting malnutrition and elucidate new roles for ankyrin-repeat proteins in plants. One sentence summaryMutations in a novel, ankyrin domain protein and genetic modifiers of a known mutation in a seed storage protein lead to increased digestibility of seed proteins in sorghum after wet cooking.

plant biology↗

bioRxiv2018

The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with gene expression in sesame

DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum L.) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, a property attributed to its presumed origin in Africa or India. Understanding DNA methylation patterns in sesame under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying its contrasting responses to these principal abiotic stresses. Here, we combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, gene expression alteration, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes under control, stress and recovery conditions. Our data showed that drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging decreased the level of methylation under stress but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the differentially expressed genes (DEGs) were highly correlated with the methylation patterns. We observed that DM was associated with the up-regulation of the DEGs while DNM was correlated with the down-regulation of the DEGs. In addition, we sequenced 44 differentially methylated regions of which 90% overlapped with the promoters and coding sequences of the DEGs. Altogether, we demonstrated that sesame has divergent epigenetic programs that respond to drought and waterlogging stresses. Our results also highlighted the possible interplay among DNA methylation and gene expression, which may modulate the contrasting responses to drought and waterlogging in sesame.

plant biology↗

bioRxiv2017

Identification of genetic factors controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp)

Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, flowering time, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine domestication-related traits. Candidate genes underlying each of those 16 QTL were identified. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programs.\n\nKey messageThis study identified regions of the cowpea genome that played an important role in cowpea domestication, including a hotspot region for increased organ size

genetics↗

bioRxiv2017

A multi-parent advanced generation inter-cross population for genetic analysis of multiple traits in cowpea (Vigna unguiculata L. Walp.)

Development and analysis of Multiparent Advanced Generation Inter-Cross (MAGIC) populations have been conducted with several crop plants to harness the potential for dissecting the genetic structure of traits and improving breeding populations. We developed a first MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents which are genetically diverse and carry many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in sub-Saharan Africa (SSA) where cowpea is vitally important in the human diet and in local economies. The eight parents were inter-crossed using structured matings to ensure the population would have balanced representation from each of the founder parents, followed by single-seed descent, resulting in 365 F8 recombinant inbred lines (RILs) each carrying a mosaic of genome blocks contributed from all founders. This was confirmed by SNP genotyping with the cowpea Illumina 60K iSelect BeadArray. Following filtering to eliminate duplicates, sister lines and accidental selfing events, a core set of 305 F8 RILs was chosen as the primary population. The F8 lines were on average 99.74% homozygous while also diverse in agronomic traits including flowering time, growth habit, maturity, yield potential and seed characteristics across environments. Trait-associated SNPs were identified for most of the parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by genetic mapping in biparental RIL populations. The distribution of recombination frequency varied considerably between chromosomes, with recombination hotspots distributed mostly in the telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain and high-resolution genetic mapping for gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.

genetics↗