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PNAS:苦瓜基因组及群体重测序

已有 541 次阅读 2020-5-30 09:16 |个人分类:每日摘要|系统分类:论文交流

Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication

第一作者Hideo Matsumura

第一单位日本信州大学

通讯作者Cheng-Ruei Lee


 Abstract 


背景回顾与问题The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes.


主要研究:Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domestication example, bitter gourd (Momordica charantia), an important Asian vegetable and medicinal plant of the family Cucurbitaceae.


结果:Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the separation of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progenitors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selection happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions.


结论:Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors.


 摘  要 


数量性状的遗传结构由孟德尔因素和多基因因素同时控制,然而,目前有关植物驯化的经典研究集中在新突变的孟德尔基因选择性清除。本文中,作者报道了葫芦科的一个重要亚洲蔬菜和药用植物,即苦瓜(Momordica charantia)的染色级别基因组组装以及非经典驯化案例。群体重测序显示野生种与亚洲栽培种大约在六千年前分化,而后大约在八百年前分化形成了东南亚栽培种,而这种新形成的栽培种与野生祖先具有更多的极端性状差异,并且在果实性状上表现出更强的选择迹象。与一些作物中的情况不同,苦瓜最大的表型差异并不是出现在野生祖先种与现代栽培种之间,而是出现在两个地区栽培种之间,反应了不同地区对于苦瓜的消费性状选择差异。另外,除了育种过程中提高雌花比例以获得更多结实,一个雌雄同体基因座在单倍群中表现出复杂的平衡多态性模式,并且在单倍群中的选择性清除信号很有可能反应了人工选择以及栽培种向野生种的遗传渗入。本文的研究突出了研究这种非经典植物驯化的重要性,显示植物驯化过程中,除了对孟德尔因素的经典选择性清除外,还存在平衡选择和多基因性状结构的信号。


 通讯作者 


**Cheng-Ruei Lee**


个人简介:

杜克大学,博士。


研究方向:

杂草植物演化背后的遗传和基因组变化


doi: 10.1073/pnas.1921016117


Journal: PNAS

Published date: May 27, 2020



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