AUTHOR=Liu Jindong , Zhan Junhui , Chen Jingguang , Lu Xiang , Zhi Shuai , Ye Guoyou 

TITLE=Validation of Genes Affecting Rice Grain Zinc Content Through Candidate Gene-Based Association Analysis

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.701658

DOI=10.3389/fgene.2021.701658

ISSN=1664-8021

ABSTRACT=<p>Several key genes governing Zn homeostasis and grain zinc content (GZC) have been functionally characterized. However, the effects of these genes in diverse breeding populations have not been evaluated; thus, their availability in breeding is unclear. In this study, the effects of 65 genes related to rice zinc responses on GZC were evaluated using two panels of breeding lines, and the superior haplotypes were identified. One panel consisted of mega varieties from the International Rice Research Institute (IRRI), South Asia, and Southeast Asia (SEA), and the other panel is breeding lines/varieties from South China (SC). In addition, a multiparent advanced generation intercross (MAGIC) population, named as DC1, was also employed. Three analytical methods, single-locus mixed linear model (SL-MLM), multilocus random-SNP-effect mixed linear model (mrMLM), and haplotype-based association analysis (Hap-AA), were applied. <italic>OsIDEF1</italic> (which explained 12.3% of the phenotypic variance) and <italic>OsZIFL7</italic> (8.3–9.1%), <italic>OsZIP7</italic> (18.9%), and <italic>OsIRT1</italic> (17.9%) were identified by SL-MLM in SEA and SC, respectively, whereas no gene was significantly associated with GZC in DC1. In total, five (<italic>OsNRAMP6</italic>, <italic>OsYSL15</italic>, <italic>OsIRT1</italic>, <italic>OsIDEF1</italic>, and <italic>OsZIFL7</italic>, 7.70–15.39%), three (<italic>OsFRDL1</italic>, <italic>OsIRT1</italic>, and <italic>OsZIP7</italic>, 11.87–17.99%), and two (<italic>OsYSL7</italic> and <italic>OsZIP7</italic>, 9.85–10.57%) genes were detected to be significantly associated with GZC in SEA, SC, and DC1 by mrMLM, respectively. Hap-AA indicated that <italic>Hap1-OsNRAMP5</italic>, <italic>Hap5-OsZIP4</italic>, <italic>Hap1-OsIRT1</italic>, <italic>Hap3-OsNRAMP6</italic>, <italic>Hap6-OsMTP1</italic>, and <italic>Hap6-OsYSL15</italic> had the largest effects for GZC in SEA, whereas <italic>Hap3-OsOPT7</italic>, <italic>Hap4-OsIRT2</italic>, <italic>Hap4-OsZIP7</italic>, <italic>Hap5-OsIRT1</italic>, and <italic>Hap5-OsSAMS1</italic> were the most significant in the SC population. Besides, superior alleles were also identified for the significant genes. The genes significantly associated with GZC and their superior haplotypes identified in different panels could be used in enhancing GZC through molecular breeding, which could further address the problem of Zn malnutrition among rice consumers.</p>