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Genome-Wide Association Analysis Identifies Candidate Loci for Callus Induction in Rice (Oryza sativa L.)

Authors :
Wintai Kamolsukyeunyong
Yeetoh Dabbhadatta
Aornpilin Jaiprasert
Burin Thunnom
Wasin Poncheewin
Samart Wanchana
Vinitchan Ruanjaichon
Theerayut Toojinda
Parichart Burns
Source :
Plants, Vol 13, Iss 15, p 2112 (2024)
Publication Year :
2024
Publisher :
MDPI AG, 2024.

Abstract

Callus induction (CI) is a critical trait for transforming desirable genes in plants. A genome-wide association study (GWAS) analysis was conducted on the rice germplasms of 110 Indica rice accessions, in which three tissue culture media, B5, MS, and N6, were used for the CI of those rice panels’ mature seeds. Seven quantitative trait loci (QTLs) on rice chromosomes 2, 6, 7, and 11 affected the CI percentage in the three media. For the B5 medium, one QTL (qCI–B5–Chr6) was identified on rice chromosome 6; for the MS medium, two QTLs were identified on rice chromosomes 2 and 6 (qCI–MS–Chr2 and qCI–MS–Chr6, respectively); for the N6 medium, four QTLs were identified on rice chromosomes 6, 7, and 11 (qCI–N6–Chr6.1 and qCI–N6–Chr6.2, qCI–N6–Chr7, and qCI–N6–Chr11, respectively). Fifty-five genes were identified within the haplotype blocks corresponding to these QTLs, thirty-one of which showed haplotypes associated with different CI percentages in those media. qCI–B5–Chr6 was located in the same region as qCI–N6–Chr6.2, and the Caleosin-related family protein was also identified in this region. Analysis of the gene-based haplotype revealed the association of this gene with different CI percentages in both B5 and N6 media, suggesting that the gene may play a critical role in the CI mechanism. Moreover, several genes, including those that encode the beta-tubulin protein, zinc finger protein, RNP–1 domain-containing protein, and lysophosphatidic acid acyltransferase, were associated with different CI percentages in the N6 medium. The results of this study provide insights into the potential QTLs and candidate genes for callus induction in rice that contribute to our understanding of the physiological and biochemical processes involved in callus formation, which is an essential tool in the molecular breeding of rice.

Details

Language :
English
ISSN :
22237747
Volume :
13
Issue :
15
Database :
Directory of Open Access Journals
Journal :
Plants
Publication Type :
Academic Journal
Accession number :
edsdoj.3f1a1401029a4c9382b36cfab767e4ca
Document Type :
article
Full Text :
https://doi.org/10.3390/plants13152112