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Designing climate-resilient rice with ideal grain quality suited for high-temperature stress.

ABSTRACT: To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in the grain. This review highlights the knowledge gained through gene discovery via quantitative trait locus (QTL) cloning and structural-functional genomic strategies to reduce chalk, increase head rice yield, and develop stable lines with optimum grain quality in challenging environments. The newly discovered genes and the knowledge gained on the influence of specific alleles related to stability of grain quality attributes provide a robust platform for marker-assisted selection in breeding to design heat-tolerant rice varieties with superior grain quality. Using the chalkiness trait in rice as a case study, we demonstrate here that the emerging field of systems genetics can help fast-track the identification of novel alleles and gene targets that can be pyramided for the development of environmentally robust rice varieties that possess improved grain quality.

SUBMITTER: Sreenivasulu N

PROVIDER: S-EPMC4669556 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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Designing climate-resilient rice with ideal grain quality suited for high-temperature stress.

Sreenivasulu Nese N Butardo Vito M VM Misra Gopal G Cuevas Rosa Paula RP Anacleto Roslen R Kavi Kishor Polavarpu B PB

Journal of experimental botany 20150205 7

To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in ...[more]

PMID: 25662847

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Project description:To dissect the genetic complexity of rice grain yield (GY) and quality in response to heat stress at the reproductive stage, a diverse panel of 190 rice accessions in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) diversity panel were treated with high nighttime temperature (HNT) stress at the reproductive stage of panicle initiation. The quantifiable yield component response traits were then measured. The traits, panicle length (PL), and number of spikelets per panicle (NSP) were evaluated in subsets of the panel comprising the rice subspecies Oryza sativa ssp. Indica and ssp. Japonica. Under HNT stress, the Japonica ssp. exhibited lower reductions in PL and NSP and a higher level of genetic variation compared with the other subpopulations. Whole genome sequencing identified 6.5 million single nucleotide polymorphisms (SNPs) that were used for the genome-wide association studies (GWASs) of the PL and NSP traits. The GWAS analysis in the Combined, Indica, and Japonica populations under HNT stress identified 83, 60, and 803 highly significant SNPs associated with PL, compared to the 30, 30, and 11 highly significant SNPs associated with NSP. Among these trait-associated SNPs, 140 were coincident with genomic regions previously reported for major GY component quantitative trait loci (QTLs) under heat stress. Using extents of linkage disequilibrium in the rice populations, Venn diagram analysis showed that the highest number of putative candidate genes were identified in the Japonica population, with 20 putative candidate genes being common in the Combined, Indica and Japonica populations. Network analysis of the genes linked to significant SNPs associated with PL and NSP identified modules that were involved in primary and secondary metabolisms. The findings in this study could be useful to understand the pathways/mechanisms involved in rice GY and its components under HNT stress for the acceleration of rice-breeding programs and further functional analysis by molecular geneticists.

Dataset Information

Designing climate-resilient rice with ideal grain quality suited for high-temperature stress.

Publications

Designing climate-resilient rice with ideal grain quality suited for high-temperature stress.

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