LRR-RLK基因启动子自然变异位点与甜瓜种子大小相关

doi:10.1016/j.jia.2024.07.012

Journal of Integrative Agriculture ›› 2024, Vol. 23 ›› Issue (10): 3522-3536.DOI: 10.1016/j.jia.2024.07.012

LRR-RLK基因启动子自然变异位点与甜瓜种子大小相关

收稿日期:2023-08-03 接受日期:2024-04-24 出版日期:2024-10-20 发布日期:2024-09-11

An allelic variation in the promoter of the LRR-RLK gene, qSS6.1, is associated with melon seed size

Xiaoxue Liang^1*, Jiyu Wang^1*, Lei Cao1, Xuanyu Du¹, Junhao Qiang¹, Wenlong Li¹, Panqiao Wang^1,2, Juan Hou^{1, 2}, Xiang Li^{1, 2}, Wenwen Mao^{1, 2}, Huayu Zhu^{1, 2}, Luming Yang^{1, 2, 3}, Qiong Li^{1, 2#}, Jianbin Hu^{1, 2, 3#}

¹College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
²Henan Engineering Research Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou 450002, China
³International Joint Laboratory of Henan Horticultural Crop Biology, Zhengzhou 450002, China

Received:2023-08-03 Accepted:2024-04-24 Online:2024-10-20 Published:2024-09-11
About author:Xiaoxue Liang, E-mail: liang951217@126.com; Jiyu Wang, E-mail: wangjiyu662022@163.com; #Correspondence Qiong Li, E-mail: chenxiao@henau.edu.cn; Jianbin Hu, E-mail: jianbinhu@henau.edu.cn * These authors contributed equally to this study.
Supported by:
This research was funded by the Henan Special Funds for Major Science and Technology, China (221100110400), the Henan Scientific and Technological Joint Project for Agricultural Improved Varieties, China (2022010503), and the National Natural Science Foundation of China (31902038 and 32072564).

摘要/Abstract

摘要：

种子大小是甜瓜中一个重要的农艺性状，直接影响种子萌发及幼苗生长。然而，关于甜瓜种子大小的遗传机制尚不清楚。在本研究中，我们采用BSA-seq方法在第6号染色体上鉴定到与种子大小相关的候选区域（约1.35 Mb）。该区域被三个不同环境下的F₂群体的种子大小相关性状QTL定位所证实。QTL定位结果鉴定到9个QTL，将其在第6号染色体上的重叠区域命名为qSS6.1。在qSS6.1区段开发新的InDel标记并对大分离群体进行基因分型，最终将目标区段精细定位到68.35 kb区间内，该区间包含8个注释基因。对候选基因的序列进行分析发现，一个注释为富含亮氨酸重复序列型(LRR)类受体蛋白激酶（LRR-RLK）的MELO3C014002基因的启动子区域中存在一个C到T的碱基突变。该突变影响了MELO3C014002基因启动子活性，且能够准确区分大籽型材料（C等位基因）和小籽型材料（T等位基因）。qRT-PCR分析表明该候选基因在两个亲本不同组织中的表达量存在显著差异。该基因的预测蛋白具有典型的LRR-RLK家族结构域，系统发育分析表明它与不同物种的同源基因具有相似性。综上可知，多方面研究结果表明候选基因MELO3C014002可能参与调控甜瓜种子大小。本研究结果有助于理解甜瓜种子大小调控机制，为通过分子育种方法改良该性状奠定了基础。

Abstract:

Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth. However, the genetic mechanism underlying seed size in melon remains unclear. In the present study, we employed Bulked-Segregant Analysis sequencing (BSA-seq) to identify a candidate region (~1.35 Mb) on chromosome 6 that corresponds to seed size. This interval was confirmed by QTL mapping of three seed size-related traits from an F₂ population across three environments. This mapping region represented nine QTLs that shared an overlapping region on chromosome 6, collectively referred to as qSS6.1. New InDel markers were developed in the qSS6.1 region, narrowing it down to a 68.35 kb interval that contains eight annotated genes. Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002, a leucine-rich repeat receptor-like kinase (LRR-RLK) gene. This mutation affected the promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions (C-allele) from the small-seeded accessions (T-allele). qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines. Its predicted protein has typical LRR-RLK family domains, and phylogenetic analyses reveled its similarity with the homologs in several plant species. Altogether, these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation. Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways.

Key words: melon , QTL mapping , seed size , candidate gene , allelic variation

Xiaoxue Liang, Jiyu Wang, Lei Cao, Xuanyu Du, Junhao Qiang, Wenlong Li, Panqiao Wang, Juan Hou, Xiang Li, Wenwen Mao, Huayu Zhu, Luming Yang, Qiong Li, Jianbin Hu. LRR-RLK基因启动子自然变异位点与甜瓜种子大小相关[J]. Journal of Integrative Agriculture, 2024, 23(10): 3522-3536.

Xiaoxue Liang, Jiyu Wang, Lei Cao, Xuanyu Du, Junhao Qiang, Wenlong Li, Panqiao Wang, Juan Hou, Xiang Li, Wenwen Mao, Huayu Zhu, Luming Yang, Qiong Li, Jianbin Hu. An allelic variation in the promoter of the LRR-RLK gene, qSS6.1, is associated with melon seed size[J]. Journal of Integrative Agriculture, 2024, 23(10): 3522-3536.

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LRR-RLK基因启动子自然变异位点与甜瓜种子大小相关

An allelic variation in the promoter of the LRR-RLK gene, qSS6.1, is associated with melon seed size

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