Variability of grain quality in sorghum: association with polymorphism in Sh2, Bt2, SssI, Ae1, Wx and O2

Abstract

To ensure food security in Africa and Asia, developing sorghum varieties with grain quality that matches consumer demand is a major breeding objective that requires a better understanding of the genetic control of grain quality traits. The objective of this targeted association study was to assess whether the polymorphism detected in six genes involved in synthesis pathways of starch (Sh2, Bt2, SssI, Ae1, and Wx) or grain storage proteins (O2) could explain the phenotypic variability of six grain quality traits [amylose content (AM), protein content (PR), lipid content (LI), hardness (HD), endosperm texture (ET), peak gelatinization temperature (PGT)], two yield component traits [thousand grain weight (TGW) and number of grains per panicle (NBG)], and yield itself (YLD). We used a core collection of 195 accessions which had been previously phenotyped and for which polymorphic sites had been identified in sequenced segments of the six genes. The associations between gene polymorphism and phenotypic traits were analyzed with Tassel. The percentages of admixture of each accession, estimated using 60 RFLP probes, were used as cofactors in the analyses, decreasing the proportion of false-positive tests (70%) due to population structure. The significant associations observed matched generally well the role of the enzymes encoded by the genes known to determine starch amount or type. Sh2, Bt2, Ae1, and Wx were associated with TGW. SssI and Ae1 were associated with PGT, a trait influenced by amylopectin amount. Sh2 was associated with AM while Wx was not, possibly because of the absence of waxy accessions in our collection. O2 and Wx were associated with HD and ET. No association was found between O2 and PR. These results were consistent with QTL or association data in sorghum and in orthologous zones of maize. This study represents the first targeted association mapping study for grain quality in sorghum and paves the way for marker-aided selection.

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

“…2A). Of six starch-related genes previously studied as a priori candidates for domestication loci (15,28), two are found at regions with notably low heterozygosity ( Fig. 2A).…”

“…2A). The starch biosynthesis enzyme brittle endosperm 2 (bt2) gene, which has been shown to be a likely domestication locus in maize (28) and sorghum (15), is at the base of the low heterozygosity region on chromosome 7. The size of this low diversity region and extensive LD (Fig.…”

“…2C) or the presence of additional loci under selection. Another a priori domestication candidate from starch metabolic pathways, transcription factor opaque2 (15), is found at the base of a low heterozygosity region on chromosome 2. Lastly, another recently identified domestication locus, the shattering gene Sh1, is found at the edge of a region with moderately, but not strikingly, lower heterozygosity, consistent with the observation that nonshattering alleles are found on at least three haplotypes in domesticated sorghums (29).…”

“…In addition, genome-wide association studies (GWAS) have been used to elucidate the genetic basis of agronomic traits in rice (12) and maize (10). Nucleotide diversity scans (13,14) and association studies (5,15) have been carried out in sorghum, but the resolution and sensitivity of these studies has been limited by the small number of markers (14). Thus, compared with maize and rice, less is known about the genetic basis of agronomic traits in sorghum.…”

Effects of Malting Conditions to Quality of Germinated Red Sorghum

“…The used grains were ranged as large grains whose weight of 1000 grain was 31.6 g. Depending on sorghum variety, this value normally varied between 7.3 and 44.2 g [5]. The grain contained very low level of maltose, glucose and amylase activity.…”