Genetic Structure and Linkage Disequilibrium in a Diverse, Representative Collection of the C4 Model Plant, Sorghum bicolor

Abstract

To facilitate the mapping of genes in sorghum [Sorghum bicolor (L.) Moench] underlying economically important traits, we analyzed the genetic structure and linkage disequilibrium in a sorghum mini core collection of 242 landraces with 13,390 single-nucleotide polymorphims. The single-nucleotide polymorphisms were produced using a highly multiplexed genotyping-by-sequencing methodology. Genetic structure was established using principal component, Neighbor-Joining phylogenetic, and Bayesian cluster analyses. These analyses indicated that the mini-core collection was structured along both geographic origin and sorghum race classification. Examples of the former were accessions from Southern Africa, East Asia, and Yemen. Examples of the latter were caudatums with widespread geographical distribution, durras from India, and guineas from West Africa. Race bicolor, the most primitive and the least clearly defined sorghum race, clustered among other races and formed only one clear bicolor-centric cluster. Genome-wide linkage disequilibrium analyses showed linkage disequilibrium decayed, on average, within 10−30 kb, whereas the short arm of SBI-06 contained a linkage disequilibrium block of 20.33 Mb, confirming a previous report of low recombination on this chromosome arm. Four smaller but equally significant linkage disequilibrium blocks of 3.5−35.5 kb were detected on chromosomes 1, 2, 9, and 10. We examined the genes encoded within each block to provide a first look at candidates such as homologs of GS3 and FT that may indicate a selective sweep during sorghum domestication.

Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems

“…We correlated structure membership coefficients obtained for the same accessions generated by InStruct and STRUCTURE and between STRUCTURE generated memberships inferred on the basis of the 13,390 SNPs from ref. 13 and our 19 SSRs for 139 common accessions using R (www.r-project.org/). Spatially explicit Bayesian modeling was done on the 138 genebank accessions for which latitude and longitude data were available using the program GENELAND (42).…”

Development and application of a 20K SNP array in potato

“…In the literature only relatively high averages of short range LD values have been reported, for example in crop species such as wheat (Würschum et al 2013)and maize (Yan et al 2009), where average initial LD of r 2 = 0.32 and r 2 = 0.24 respectively were observed, in (Wang et al 2013) even averages of r 2 = 0.5 are observed. We observed a lower average r 2 for short range LD in our data (r 2 is between 0.19 and 0.22).…”

“…In many studies a restriction on the MAF is applied, where a 5% cutoff is most commonly used (Zhao et al 2011;Delourme et al 2013;Esteras et al 2013;Wang et al 2013;Würschum et al 2013;Adetunji et al 2014;Li et al 2014). In some cases a 10% (Hyten et al 2007;Comadran et al 2011) or even a 20% cut-off (Branca et al 2011) is used.…”

Initiation of Setaria as a model plant

“…However, in the genomics era, the large genome size of maize combined with its paleopolyploid evolutionary history and the shear size of adult maize plants present challenges for functional genomics research. Sorghum is also considered as a model for C 4 functional genomics study [10], but its adult plant size and longer life cycle made it difficult for lab management. Switchgrass and napiergrass are considered putative biofuel crops, but their polyploid backgrounds make their functional genomics study difficult, so is the situation to common millet, an ancient cereal which is still widely grown in dry land area in the world.…”