Dissecting the genome-wide genetic variants of milling and appearance quality traits in rice. (30th May 2019)

• Record Type: Journal Article
• Authors: Misra, Gopal; Anacleto, Roslen; Badoni, Saurabh; Butardo, Vito; Molina, Lilia; Graner, Andreas; Demont, Matty; Morell, Matthew K; Sreenivasulu, Nese
• Editors: Rebetzke, Greg
• Is Part Of: Journal of experimental botany. Volume 70:Number 19(2019)
• Page Start: 5115
• Page End: 5130
• Publication Date: 2019-05-30
• Subjects: Genome-wide association studies -- grain chalkiness -- head rice yield -- market survey -- multi-locus GWAS -- whole-genome resequencing; Botany -- Periodicals; Botany, Experimental -- Periodicals; Plant physiology -- Periodicals; 580
• DOI: 10.1093/jxb/erz256
• Languages: English
• ISSNs: 0022-0957

Abstract

Abstract : Genetic regions in the rice genome are identified that affect the proportion of grains that remain intact after milling (the head rice yield) and the degree of chalkiness in the grain. Abstract: Higher head rice yield (HRY), which represents the proportion of intact grains that survive milling, and lower grain chalkiness (opacity) are key quality traits. We investigated the genetic basis of HRY and chalkiness in 320 diverse resequenced accessions of indica rice with integrated single- and multi-locus genome-wide association studies using 2.26 million single-nucleotide polymorphisms. We identified novel haplotypes that underly higher HRY on chromosomes 3, 6, 8, and 11, and that lower grain chalkiness in a fine-mapped region on chromosome 5. Whole-genome sequencing of 92 IRRI breeding lines was performed to identify the genetic variants of HRY and chalkiness. Rare and novel haplotypes were found for lowering chalkiness, but missing alleles hindered progress towards enhancing HRY in breeding material. The novel haplotypes that we identified have potential use in breeding programs aimed at improving these important traits in the rice crop.