基于GWAS和多组学联合分析定位石榴籽粒硬度相关基因

Pomegranate (Punica granatum L.) is an important economic tree because of its high commercial and medicinal values. Soft-seeded pomegranate is easy to swallow and fetch high price in the market as compared to hard seeded. The demand of the soft seeded pomegranate by the farmers and the consumers is extremely high. Tunisia is the only one commercial variety introduced from Tunisia since 1986. The problem of single variety and depression seriously restricts the development of pomegranate industry. Breeding for the new soft-seeded varieties will contribute to optimize the industrial structure of trees and the targeted poverty alleviation. Identification of the genes responsible to soft seed will be conducive to marker breeding programs in pomegranate. Zhengzhou Fruit Research Institute is a leading research institute of the country which has more than 300 genetic diversity of pomegranates collected from different geographical regions of the country as well as from other countries. Recently，we have investigated the genetic mechanism underlying pomegranate seed hardness by comparing differential gene expression, protein expression profiles and metabolin between soft- and hard-seeded varieties. Correspondingly, we identified many quantitative trait loci related to the seed hardness. The objective of this project is to develop genome-wide association mapping (GWAS) to identify the genes related to the seed hardness in pomegranates. The results of population genetic mapping are combined with the muti-omics analysis to select the candidate genes associated with the seed hardness. Then we will clone the candidate genes to develop the molecular markers. Implementation of this project can characterize the causal genes related to the seed hardness, then develop molecular markers to facilitate selection of better genotypes of soft-seeded traits.

石榴有着巨大的经济效益以及药用价值，是一种重要的新兴经济树种。软籽石榴籽粒退化易于吞咽，深受广大果农和消费者喜爱，市场广阔。目前，突尼斯石榴是国内唯一真正意义上的软籽栽培品种，其品种单一老化的问题严重制约了石榴产业的发展。培育软籽石榴新品种不仅有利于经果林产业结构优化，对发展特色林果精准扶贫具有重要意义。定位籽粒硬度形成基因应用于分子标记辅助选择育种，可以加快育种效率。项目申报单位前期收集了300多份不同地理分布的遗传多样性石榴资源。项目组成员比较研究了软籽和硬籽品种间籽粒的基因表达、蛋白质丰度及代谢物差异，筛选了大量与籽粒硬度相关QTL。本项目拟进一步采用全基因组关联分析策略定位籽粒硬度相关基因；结合转录组学、蛋白质组学以及代谢组学数据筛选候选基因；克隆候选基因，开发特异性分子标记。本项目的实施将有利于发掘籽粒硬度关键候选基因，为开发分子标记辅助选择优良基因型提供理论基础。

石榴是世界上一古老的果树树种。因其巨大的经济效益以及药用价值，石榴，尤其是软籽石榴品种，逐渐成为了新兴的经济树种。鉴定决定籽粒硬度形成的关键基因有利于分子标记辅助选育软籽石榴新品种。本研究通过对286份石榴种质资源进行群体结构及遗传多样性分析，发现软籽群体和硬籽群体存在着明显的分层现象；采用GWAS结合多组学的方法定位了25个与籽粒硬度相关候选基因，其中MYB (Pg01g46990)，Pg01g46850和Pg08g282710被先前研究结果证实通过参与细胞壁结构形成调控石榴籽粒硬度；另外，Pg01g46630在石榴籽粒内种皮中差异表达参与调控脂质蛋白合成，从而影响籽粒硬度；通过基因家族分析以及遗传转化实验，证实PgL0145810.1启动子区MYB反座子可能通过调控其差异表达，进而控制木质部结构来影响籽粒硬度。本项目的实施为解析籽粒硬度形成机制以及分子标记辅助选育软籽石榴新品种提供了重要理论参考。

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