A Novel Allele in the Promoter of Wx Decreases Gene Expression and Confers Lower Apparent Amylose Contents in Japonica Rice (Oryza sativa L.)

文献类型： 外文期刊

第一作者： Tang, Weijie

作者： Tang, Weijie;Chen, Haiyuan;Zhang, Suobing;Tang, Jun;Lin, Jing;Fang, Xianwen;Zhang, Yunhui;Tang, Weijie;Chen, Haiyuan;Zhang, Suobing;Tang, Jun;Lin, Jing;Fang, Xianwen;Zhang, Yunhui;Chen, Gaoming;Zhang, Yunhui

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关键词： Wx; promoter; allele; AAC; japonica rice; nitrogen

期刊名称：PLANTS-BASEL （ 影响因子：4.5； 五年影响因子：4.8 ）

ISSN： 2223-7747

年卷期： 2024 年 13 卷 5 期

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收录情况： SCI

摘要： Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wx(b) is the major allele in japonica and produces moderate AC (15 similar to 18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR-Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wx(b) and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wxb) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs.

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