ABSTRACT
BACKGROUND: Photoperiod-sensitive flowering is a key adaptive trait for sorghum (Sorghum bicolor) in West and Central Africa. In this study we performed an association analysis to investigate the effect of polymorphisms within the genes putatively related to variation in flowering time on photoperiod-sensitive flowering in sorghum. For this purpose a genetically characterized panel of 219 sorghum accessions from West and Central Africa was evaluated for their photoperiod response index (PRI) based on two sowing dates under field conditions. RESULTS: Sorghum accessions used in our study were genotyped for single nucleotide polymorphisms (SNPs) in six genes putatively involved in the photoperiodic control of flowering time. Applying a mixed model approach and previously-determined population structure parameters to these candidate genes, we found significant associations between several SNPs with PRI for the genes CRYPTOCHROME 1 (CRY1-b1) and GIGANTEA (GI). CONCLUSIONS: The negative values of Tajima's D, found for the genes of our study, suggested that purifying selection has acted on genes involved in photoperiodic control of flowering time in sorghum. The SNP markers of our study that showed significant associations with PRI can be used to create functional markers to serve as important tools for marker-assisted selection of photoperiod-sensitive cultivars in sorghum.
Subject(s)
Flowers/genetics , Genes, Plant , Photoperiod , Sorghum/genetics , Africa, Central , Africa, Western , Chromosome Mapping , Chromosomes, Plant/genetics , Chromosomes, Plant/metabolism , Cryptochromes/genetics , Flowers/metabolism , Flowers/physiology , Genetic Association Studies , Genetic Markers , Linkage Disequilibrium , Models, Biological , Phenotype , Plant Proteins/genetics , Plant Proteins/metabolism , Polymorphism, Single Nucleotide , Selection, Genetic , Sorghum/metabolism , Sorghum/physiology , Species Specificity , Time FactorsABSTRACT
Accounting for population structure to minimize spurious associations in association analyses is of crucial importance. With sorghum genomic sequence information being available, there is a growing interest in performing such association studies for a number of important agronomic traits using a candidate gene approach. The aims of our study were to conduct a systematic survey of molecular genetic diversity and analyze the population structure in cultivated sorghum [Sorghum bicolor (L.) Moench] accessions from West Africa. Our analysis included 219 West African cultivated sorghum accessions with differing maturity intended for a marker-trait association study. A total of 27 SSRs were used, which resulted in detection of 513 alleles. Genetic diversity estimates for the accessions were found to be high. The accessions were divided into two subgroups using a model-based approach. Our findings partly agree with previous studies in that the guinea race accessions could be distinguished clearly from other accessions included in the analysis. Race and geographical origin of the accessions may be responsible for the structure we observed in our material. The extent of linkage disequilibrium for all combinations of SSRs was in agreement with expectations based on the mating system.
Subject(s)
Genetic Variation/genetics , Sorghum/genetics , Africa, Western , Alleles , Computer Simulation , Genetics, Population , Genome, Plant/genetics , Genotype , Linkage Disequilibrium , Tandem Repeat Sequences/geneticsABSTRACT
The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineënse accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discussed.
