Journal
JOURNAL OF EXPERIMENTAL BOTANY
Volume 71, Issue 14, Pages 4188-4200Publisher
OXFORD UNIV PRESS
DOI: 10.1093/jxb/eraa182
Keywords
Abiotic stress; genetic diversity; GWAS; population structure; rice; West Africa
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Funding
- West Africa Agricultural Productivity Programme (WAAPP)/WAAPP Phase II/2013 PhD scholarship
- International Foundation for Sciences/IFS Grant [C/5878-1]
- McCouch RiceLab at Cornell University
- National Science Foundation Graduate Research Fellowship [DGE-1144153]
- USDA NIFA [2014-67003-21858]
- NIFA [2014-67003-21858, 687469] Funding Source: Federal RePORTER
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Adoption of rice varieties that perform well under high iron-associated (HIA) stress environments can enhance rice production in West Africa. This study reports the genetic characterization of 323 rice accessions and breeding lines cultivated in West Africa using genotyping-by-sequencing and their phenotypic response to HIA treatments in hydroponic solution (1500 mg l(-1) FeSO4 center dot 7H(2)O) and hot-spot fields. The germplasm consisted of four genetic subpopulations: Oryza glaberrima (14%), O. sativa japonica (7%), O. sativa-indica Group 1 (45%), and O. sativa-indica Group 2 (25%). Severe versus mild stress in the field was associated with a reduced SPAD value (12%), biomass (56%), and grain yield (57%), with leaf bronzing explaining 30% and 21% of the variation for biomass and grain yield, respectively. Association mapping using 175 indica genotypes identified 23 significant single nucleotide polymorphism (SNP) markers that mapped to 14 genomic regions. Genome-wide association study (GWAS) signals associated with leaf bronzing, a routinely used indicator of HIA stress, differed in hydroponic compared with field conditions. Contrastingly, six significant SNPs on chromosomes 8 and 9 were associated with the SPAD value under HIA stress in both field and hydroponic experiments, and a candidate potassium transporter gene mapped under the peak on chromosome 8. This study helps define criteria for assessing rice performance under HIA environments.
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