A genomics resource for genetics, physiology, and breeding of West African sorghum.

Jacques M Faye,Daniel Fonceka,Eyanawa A Akata,Bassirou Sine,Sophie Bouchet,Fanna Maina,Niaba Teme,Jean‐Francois Rami,Aissata Mamadou,Sandeep Marla,Geoffrey P Morris,Ndiaga Cisse,Cyril Diatta

doi:10.1002/tpg2.20075

Abstract

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 western Africa (WA) 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 (GBS) was used to generate 159,101 high-quality biallelic single nucleotide polymorphisms (SNPs), with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = .00045), only slightly less than in a global diversity panel (GDP) (π = .00055). Linkage disequilibrium (LD) decayed to background level (r2 < .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 (GWAS) of days to flowering (DFLo) and plant height (PH) 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 U.S. germplasm (Ma6 and SbCN8) suggests that photoperiodic flowering in West African sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in WA.

Highlights

Crop production in many developing countries is limited by biotic and abiotic factors that reduce food supplies to smallholder farmers in semiarid areas
A final data set of 159,101 high-quality single nucleotide polymorphism (SNP) was maintained after removing SNPs with >20% missing data, minor allele frequency (MAF) < .01, and keeping only biallelic SNPs
We determined if the 159,101 GBS SNPs have potential impacts on protein-coding sequences based on the sorghum reference sequence v.3.1

Summary

Introduction

Crop production in many developing countries is limited by biotic and abiotic factors that reduce food supplies to smallholder farmers in semiarid areas. Genetic studies contribute to the development of adapted cultivars to meet global food security and help provide enough genetic diversity suitable for efficient crop breeding (Jordan, Mace, Cruickshank, Hunt, & Henzell, 2011). The availability of high-density markers evenly distributed throughout the genome is a prerequisite for understanding genetic diversity and genetic basis of adaptive traits. Recent advances in next-generation sequencing technologies and genotyping-bysequencing (GBS) have rendered possible the generation of high-density markers with affordable low cost (Elshire et al, 2011; Poland, Brown, Sorrells, & Jannink, 2012). These tools facilitate characterization of the genetic structure of local germplasm relative to global diversity. Historical recombination along with short to moderate linkage disequilibrium (LD) existing within a diversity panel greatly improve the mapping resolution to identify novel genes and novel natural variants at known genes in major crops (Cao et al, 2016; Gapare et al, 2017; Huang et al, 2010; Yano et al, 2016; Zhao et al, 2019)

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