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Multi-model genome-wide association studies for appearance quality in rice

OAR@ICRISAT

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Relation http://oar.icrisat.org/12512/
https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1304388/full
https://doi.org/10.3389/fpls.2023.1304388
 
Title Multi-model genome-wide association studies for appearance quality in rice
 
Creator Sachdeva, S
Singh, R
Maurya, A
Singh, V K
Singh, U M
Kumar, A
Singh, G P
 
Subject Rice
 
Description Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
 
Publisher Frontiers Media
 
Date 2024-01-11
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12512/1/Frontiers%20in%20Plant%20Science_14_01-16_2024.pdf
Sachdeva, S and Singh, R and Maurya, A and Singh, V K and Singh, U M and Kumar, A and Singh, G P (2024) Multi-model genome-wide association studies for appearance quality in rice. Frontiers in Plant Science (TSI), 14. 01-16. ISSN 1664-462X