Genome-wide Association Study of Resistant Starch (RS) Phenotypes in a Barley Variety Collection

Abstract

Barley is primarily grown for feed and malt, but in some regions of the world it is also considered to be a staple food. Some barley types such as high-amylose barley have also gained importance as health-promoting foods. Starch that is not readily digested in the upper mammalian gastrointestinal system, or resistant starch (RS), is considered to be valuable because it prevents some diet-related diseases such as colon cancer. RS was quantified in a diverse collection of 209 spring barley varieties released in Europe during the past 100 years. The RS content varied from <1% to >15% in the collection, with 13 varieties having high RS content (>11%) and 15 varieties below 1%. Combined with genome-wide association scanning (GWAS), SNP markers and candidate genes controlling the RS content in grains were identified. This identified 40 SNP markers with a LOD score above 2, located on chromosomes 2H, 3H, 5H, and 6H, respectively. Among these SNPs, 10 genes with a known role in starch biosynthesis were associated on the basis of synteny conservation to the rice genome. The β-glucan content was quantified in 61 varieties selected to represent extreme as well as medium RS values. The β-glucan amount in the 15 varieties with RS <1% ranged from 1.7 to 3.2%, ranged from 1.76 to 2.54% in the 13 varieties with RS >11%, and ranged from 1.95 to 2.82% for those with 1%< RS < 11%. No statistically significant correlation between RS content and β-glucan content was found. This association analysis of commercial varieties revealed a large variation in RS content and identified a number of SNP markers that can be explored for selection and further dissection of the pathway and control of RS phenotype.

Genetic architecture of kernel composition in global sorghum germplasm

“…GWAS have identified allelic polymorphisms for important agronomic traits in cereal crops [28–32], including alleles responsible for variation in grain composition of rice [30, 32], maize [33–36], and barley [37, 38]. Linkage and association studies have identified several loci controlling sorghum grain composition [39–43], and the identification of the gene underlying the waxy mutation has been fine mapped to 1.8 Mb on chromosome 10 [44], but more work needs to be done to precisely identify genes responsible for natural variation of grain composition.…”

Characterisation of starch during germination and seedling development of a rice mutant with a high content of resistant starch

“…While the RS content in common cereals is very low (mostly below 3%) (Shu et al, 2006), a few cereal varieties and accessions with a high RS content have been reported, e.g. 15 barley varieties had RS above 11% (Shu et al, 2012) and a series of rice mutants with an enhanced RS content have been obtained through mutation breeding (Shu et al, 2009). This suggests that RS might potentially not be metabolized in cereals and therefore that a high content of RS might have a negative effect on germination and seedling development.…”

Quantification of amylose, amylopectin, and β-glucan in search for genes controlling the three major quality traits in barley by genome-wide association studies

“…Members of the GT family and glycoside hydrolase were also found to be responsible for resistant starch accumulation in a recent GWAS of barley (Shu et al, 2012). That indicated these genes might affect synthesis of starch molecular components indirectly by regulating other pathways in the metabolic network through the same substrates especially those depending on UDP-glucose (Figure 4).…”