Title: Association mapping for grain quality in a diverse sorghum collection Authors
|Sukumaran, Sivakumar -|
|Xiang, Wenwen -|
|Tuinstra, Mitchell -|
|Tesso, Tesfaye -|
|Hamblin, Martha -|
|Yu, Jianming -|
Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 20, 2012
Publication Date: November 1, 2012
Citation: Sukumaran, S., Xiang, W., Bean, S., Pedersen, J.F., Tuinstra, M.R., Tesso, T.T., Hamblin, M.T. and Yu, J. 2012. Association mapping for grain quality in a diverse sorghum collection. The Plant Genome. 5:126-135. Interpretive Summary: Grain sorghum is a genetically diverse crop, however little is known how this diversity relates to grain quality traits. To gain an understanding of the relationships between grain quality and genetic diversity in sorghum, candidate gene association mapping was used on a diverse collection of 300 sorghum accessions. Data analysis resulted in the identification of eight significant marker-trait associations including markers for grain hardness and starch synthesis genes. Knowledge on the genetic basis of grain quality traits will complement breeding efforts to improve sorghum grain quality.
Technical Abstract: Grain sorghum harbors considerable amount of genetic diversity for grain quality. It is an important criterion affecting the end use ability of sorghum grains. Knowledge on the genetic basis of grain quality traits will complement breeding efforts to improve sorghum grain quality. Candidate gene association mapping was employed on a diverse panel of 300 sorghum accessions, to assess marker-trait associations for ten grain quality traits, phenotyped through single kernel characterization system (SKCS) and near infrared reflectance spectroscopy (NIRS). The analysis of the accessions through 1290 genome-wide SNPs (single nucleotide polymorphisms) divided the panel into 5 subpopulations that corresponds to races: 3 major sorghum races (durra, kafir, and caudatum), one intermediate race guinea-caudatum, and one working group (zerazera/caudatum). These races differed in kernel hardness, acid detergent fiber, and total digestible nutrients. Analysis of marker-trait associations between 333 SNPs in candidate genes/loci and grain quality traits resulted in eight significant marker-trait associations. Among the significant SNPs associated, a SNP on starch synthase IIa (SSIIa) gene was associated with kernel hardness (KH) with a likelihood-ratio based R2 (RLR2) value of 0.08 and a SNP on loci pSB1700 was associated with a RLR2 value of 0.10. SNP on starch synthase (SSIIb) gene was associated with starch content with a RLR2 value of 0.10 and a SNP on a loci pSB1120 was associated with RLR2 value of 0.09.