title: Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis.
abstract: A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related noncommunicable diseases.
authors.affiliation: Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
authors.forename: Vito M
authors.identifier: 0000-0003-3418-2140
authors.initials: VM
authors.lastname: Butardo
authors.affiliation: Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
authors.forename: Roslen
authors.identifier: 0000-0002-0253-8774
authors.initials: R
authors.lastname: Anacleto
authors.affiliation: Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
authors.forename: Sabiha
authors.initials: S
authors.lastname: Parween
authors.affiliation: Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
authors.forename: Irene
authors.initials: I
authors.lastname: Samson
authors.affiliation: Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
authors.forename: Krishna
authors.initials: K
authors.lastname: de Guzman
authors.affiliation: Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
authors.forename: Crisline Mae
authors.initials: CM
authors.lastname: Alhambra
authors.affiliation: Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
authors.forename: Gopal
authors.initials: G
authors.lastname: Misra
authors.affiliation: Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines n.sreenivasulu@irri.org.
authors.forename: Nese
authors.identifier: 0000-0002-3998-038X
authors.initials: N
authors.lastname: Sreenivasulu
mesh_terms: D000687:Amylopectin / Q000235:genetics / Q000378:metabolism; D000688:Amylose / Q000096:biosynthesis* / Q000235:genetics; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D032461:Chromosomes, Plant; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D006239:Haplotypes; D007529:Isoflavones / Q000235:genetics / Q000378:metabolism; D012275:Oryza / Q000235:genetics* / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D015203:Reproducibility of Results; D013213:Starch / Q000235:genetics
chemical_list: D000687:Amylopectin; D000688:Amylose; D051792:Basic Helix-Loop-Helix Proteins; D007529:Isoflavones; D010940:Plant Proteins; D013213:Starch