Identification of SSR markers associated with height using pool-based genome-wide association mapping in sorghum

Abstract

Sorghum has been proposed as a potential energy crop. However, it has been traditionally bred for grain yield and forage quality, not traits related to bioenergy production. To develop tools for genetic improvement of bioenergy-related traits such as height, genetic markers associated with these traits have to be identified first. Association mapping has been extensively used in humans and in some crop plants for this purpose. However, genome-wide association mapping using the whole association panel is costly and time-consuming. A variation of this method called pool-based genome-wide association mapping has been extensively used in humans. In this variation, pools of individuals with contrasting phenotypes, instead of the whole panel, are screened with genetic markers and polymorphic markers are confirmed by screening the individuals in the pools. Here we identified several new simple sequence repeats (SSR) markers associated with height using this pool-based genome-wide association mapping in sorghum.After screening the tall and short pools of sorghum accessions from the sorghum mini core collection developed at the International Crops Research Institute for the Semi-Arid Tropics with 703 SSR markers, we have identified four markers that are closely associated with sorghum height on chromosomes 2, 6, and 9. Comparison with published maps indicates that all four markers are clustered with markers previously mapped to height or height-related traits and with candidate genes involved in regulating plant height such as FtsZ, Ugt, and GA 2-oxidase. The mapping method can be applied to other crop plants for which a high throughput genome-wide association mapping platform is not yet available.

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

“…This mini-core collection is a representative sampling of the ICRISAT core collection of 22,473 landraces, with accessions originating from 76 countries and displaying a full range of phenotypic traits displayed in the core collection (Grenier et al 2001; Upadhyaya et al 2009). The mini-core collection has been used for association mapping in sorghum using a limited number of simple sequence repeat markers (Wang et al 2011; Upadhyaya et al 2012; Wang et al 2012). Here, we re-examine the genetic structure of the ICRISAT mini core collection by using PCA, Bayesian population structure analysis and Neighbor-Joining phylogenetic analysis and subsequently analyze genome-wide LD to gain a greater understanding of the sorghum genome for the benefit of association mapping with 13,390 SNP markers.…”

Seed dormancy QTL identification across a Sorghum bicolor segregating population

“…Genomic DNA was extracted with CTAB according to Watson and Thompson (1986), and working dilutions (20 ng ll -1 ) were prepared. SSR primer pair sequences were obtained from public sorghum databases (Bhattramakki et al 2000;Kong et al 2000;Schloss et al 2002;Wang et al 2012;Li et al 2009;Brown et al 1996;Upadhyaya et al 2012) and synthesised in an external facility (Alfa DNA, Canada). Highly polymorphic SSRs were preferred to increase the chance of their being polymorphic between the parental lines used in this work.…”

Evaluation and association mapping of agronomic traits for drought tolerance in sorghum [Sorghum bicolor (L.) Moench]

“…Marker mSbCIR223 had an effect of 4.1% of the total phenotypic variation; mSbCIR248 had an effect of 5.39% of the total phenotypic variation, whereas Xtxp145 had an effect of 17.76% of the total phenotypic variation. Wang et al (2012), using pool based genome wide association mapping, reported four SSR markers that were closely associated with PHT on chromosomes 2 and 6. Similarly, Sirinivas et al (2009), using conventional method confirmed the presence of QTLs for PHT on chromosome 6 and 7 in sorghum.…”

“…In sorghum, Shehzad et al (2009) reported a total of 14 significant SSR loci associated with traits including days to heading, days to flowering, number of panicles and panicle length using 107 representative sorghum accessions and 98 SSR markers. Wang et al (2012) reported two SSR markers consistently associated with plant height at two environments. Upadhyaya et al (2012) reported significant associations of five markers with maturity date and plant height on chromosomes 6, 9, and 10 using 242 sorghum accessions and 39 SSR markers.…”