Open access resources for genome-wide association mapping in rice.
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ABSTRACT:
SUBMITTER: McCouch SR
PROVIDER: S-EPMC4742900 | biostudies-literature | 2016
REPOSITORIES: biostudies-literature
Publications
Open access resources for genome-wide association mapping in rice.
McCouch Susan R SR Wright Mark H MH Tung Chih-Wei CW Maron Lyza G LG McNally Kenneth L KL Fitzgerald Melissa M Singh Namrata N DeClerck Genevieve G Agosto-Perez Francisco F Korniliev Pavel P Greenberg Anthony J AJ Naredo Ma Elizabeth B ME Mercado Sheila Mae Q SM Harrington Sandra E SE Shi Yuxin Y Branchini Darcy A DA Kuser-Falcão Paula R PR Leung Hei H Ebana Kowaru K Yano Masahiro M Eizenga Georgia G McClung Anna A Mezey Jason J
Nature communications 20160204
Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse ...[more]
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Project description:Rice is a temperature-sensitive crop and its production is severely affected by low temperature in temperate and sub-tropical regions. To understand the genetic basis of cold tolerance in rice, we evaluated the cold tolerance at the seedling stage (CTS) of 295 rice cultivars in the rice diversity panel 1 (RDP1), these cultivars were collected from 82 countries.The evaluations revealed that both temperate and tropical japonica rice cultivars are more tolerant to cold stress than indica and AUS cultivars. Using the cold tolerance phenotypes and 44 K SNP chip dataset of RDP1, we performed genome-wide association mapping of quantitative trait loci (QTLs) for CTS. The analysis identified 67 QTLs for CTS that are located on 11 chromosomes. Fifty-six of these QTLs are located in regions without known cold tolerance-related QTLs.Our study has provided new information on the genetic architecture of rice cold tolerance and has also identified highly cold tolerant cultivars and CTS-associated SNP markers that will be useful rice improvement.
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