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Journal of Integrative Agriculture  2025, Vol. 24 Issue (12): 4496-4514    DOI: 10.1016/j.jia.2024.03.013
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Genome-wide association and co-expression uncovered ZmMYB71 controls kernel starch content in maize
Jienan Han1, Ran Li1, Ze Zhang1, 2, Shiyuan Liu1, Qianqian Liu1, Zhennan Xu1, Zhiqiang Zhou 1, Xin Lu1, Xiaochuan Shangguan1, 2, Tingfang Zhou1, 2, Jianfeng Weng1, Zhuanfang Hao1, Degui Zhang1, Hongjun Yong1, Jingyu Xu2, Mingshun Li1#, Xinhai Li1, 2#

1 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China

2 College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China

 Highlights 
A genome-wide association study (GWAS) revealed 84–96 loci linked to maize kernel starch content (SC) across two years, identifying 185 candidate genes.  Among them, ZmMYB71, a MYB-related transcription factor, showed the strongest co-expression with starch synthesis genes.
ZmMYB71 acts as a nuclear transcriptional repressor that directly downregulates key starch biosynthesis genes (Sh1, Sh2, GBSSI).  Mutants lacking ZmMYB71 exhibited a notable increase in SC (over 2.32%) without negatively affecting grain weight or amylose content.
The elite haplotype Hap1 of ZmMYB71 is more prevalent in high-starch maize groups and has increased in frequency over recent breeding stages, rising to 40.28% in post-2010 inbred lines, indicating its breeding value for improving SC.
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摘要  
淀粉是籽粒的主要贮藏物质,对玉米(Zea mays L.)的产量和品质至关重要。为满足未来粮食生产需求,了解玉米籽粒淀粉含量(SC)自然变异的遗传基础对于玉米育种意义重大。通过全基因组关联分析(GWAS),基于2年籽粒SC表型值分别发现84个和96个显著关联位点,关联区间包含185个候选基因。其中,ZmMYB71编码MYB转录因子,与淀粉合成基因共表达频数表现最高。本研究表明ZmMYB71是定位于细胞核的转录抑制因子,突变体籽粒SC增加幅度大于2.32%,但直链淀粉含量或百粒重基本不受影响。相较于野生型,zmmyb71突变体Sh1Sh2GBSSI表达量分别提高了1.56倍、1.45倍和1.32倍,与RNA测序结果一致。进一步研究表明ZmMYB71可能通过GATATC和TTAGGG基序直接抑制淀粉合成基因的启动子活性。此外,我们发现ZmMYB71优异单体型Hap1在高淀粉BSSS和PB类群占比超过55%,而在低淀粉PA类群中仅为7.14%。比较不同育种阶段Hap1单体型出现频率,在1980~1990年和2000年自交系中分别占28.57%和27.94%,而2010年后显著增加至40.28%。本研究为玉米籽粒淀粉的自然变异提供了宝贵信息,同时我们认为ZmMYB71作为负调控因子有潜力应用于玉米籽粒SC遗传改良。


Abstract  

Starch serves as a critical storage component, significantly influencing the grain yield and quality of maize (Zea mays L.).  Understanding the genetic basis of natural variation in kernel starch content (SC) is essential for maize breeding to meet future demands.  A genome-wide association study (GWAS) identified 84 and 96 loci associated with kernel SC across two years, overlapping with 185 candidate genes.  The candidate gene ZmMYB71, encoding a MYB-related transcription factor, demonstrated the highest co-expression frequency with starch synthesis genes.  Analysis revealed that ZmMYB71 functions as a nuclear located transcription repressor, and mutants exhibited increased kernel SC by over 2.32%, with minimal impact on amylose content or 100-grain weight.  Sh1, Sh2, and GBSSI exhibited up-regulation in mutants by 1.56-, 1.45- and 1.32-fold, respectively, aligning with RNA sequencing results; their promoter activities appear directly repressed by ZmMYB71 through the GATATC and TTAGGG motifs.  Additionally, the ZmMYB71 elite haplotype Hap1 occurred in over 55% of the high-starch maize sub-populations Iowa Stiff Stalk Synthetic (BSSS) and Partner B (PB), but only in 7.14% of the low-starch sub-population Partner A (PA).  Analysis of Hap1 haplotype frequencies across breeding stages revealed a significant increase to 40.28% in inbred groups released after 2010, compared to 28.57 and 27.94% in 1980 and 1990, and 2000, respectively.  These findings enhance understanding of natural variation in maize kernel SC and establish ZmMYB71 as a negative regulator with potential applications in SC improvement.

Keywords:  maize       kernel starch content        co-expression analysis        ZmMYB71        negative regulator  
Received: 28 November 2023   Accepted: 11 January 2024 Online: 02 March 2024  
Fund: We acknowledge the financial support from the National Key Research and Development Program of China (2021YFD1201004), the Science and Technology Innovation Project, Chinese Academy of Agricultural Sciences (CAAS-ZDRW202201), and the Shandong Provincial Key R&D Program, China (2023LZGC010).
About author:  #Correspondence Mingshun Li, E-mail: limingshun@caas.cn; Xinhai Li, E-mail: lixinhai@caas.cn

Cite this article: 

Jienan Han, Ran Li, Ze Zhang, Shiyuan Liu, Qianqian Liu, Zhennan Xu, Zhiqiang Zhou, Xin Lu, Xiaochuan Shangguan, Tingfang Zhou, Jianfeng Weng, Zhuanfang Hao, Degui Zhang, Hongjun Yong, Jingyu Xu, Mingshun Li, Xinhai Li. 2025. Genome-wide association and co-expression uncovered ZmMYB71 controls kernel starch content in maize. Journal of Integrative Agriculture, 24(12): 4496-4514.

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