Genome assembly and population genomic analysis reveal the genetic basis of popcorn evolution

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Xiaojian Fang, Hangqin Liu, Jiacheng Liu, Yang Song, Min Xu, Xing Jian, Li Dong, Qianwen Zhang, Le Xu, Guorui Fan, Zhaoying Wang, Yiwen You, Tianyu Feng, Wenyu Li, Yuling Li, Rentao Song, Zhongwei Lin
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Abstract

SummaryPopcorn, one of the world's most popular snack foods, represents the most ancient type of maize domesticated by humans. However, the genetic basis underlying popcorn evolution and kernel‐popping traits remains largely unknown. In this study, we assembled a high‐quality genome sequence of the popcorn landrace Strawberry Popcorn (SP) and conducted extensive population genomic analyses. The SP genome spans 2.3 Gb and harbours a large inversion on chromosome 8, along with millions of genetic variants that enable the discovery of beneficial alleles. Translocations and substantial duplications of the Ga1 gene occurred in the locus associated with unilateral cross‐incompatibility on chromosome 4. Tandemly duplicated Ga1 genes underwent pseudogenisation and truncation with complete loss of gene function. The P1 gene experienced gene expansion and regulatory modifications, leading to downregulation of transcription and subsequent loss of pericarp colour during maize domestication and improvement. Population genomic analysis further identified a subset of 12 marker genes from over 2494 genes under human selection, which were reshaped to enhance kernel‐popping traits during domestication. These marker genes include Pl1 and Dek1 for pericarp and aleurone layer thickness; THP9, Sh2, SUS1, Smk10, KW1, O7, and NKD1 for protein and starch biosynthesis; and VP5, CCD7, and Crti3 for carotene biosynthesis, which all influence endosperm vitreousness, a key factor determining kernel hardness for popping. Among these genes, KW1 and O7 stand out as pivotal genes with a significant impact on kernel‐popping performance. These results provide a wealth of gene targets to greatly accelerate the molecular breeding of improved popcorn varieties.
基因组组装和群体基因组分析揭示了爆米花进化的遗传基础
爆米花是世界上最受欢迎的休闲食品之一,代表了人类驯化的最古老的玉米品种。然而,爆米花进化和爆粒性状的遗传基础仍然未知。在这项研究中,我们组装了爆米花地方品种草莓爆米花(SP)的高质量基因组序列,并进行了广泛的群体基因组分析。SP的基因组跨度为2.3 Gb,在8号染色体上有一个大的反转,以及数百万的遗传变异,使发现有益的等位基因成为可能。Ga1基因易位和大量重复发生在4号染色体上与单侧交叉不相容相关的位点上。串联复制的Ga1基因发生假原化和截断,基因功能完全丧失。在玉米驯化和改良过程中,P1基因经历了基因扩增和调控修饰,导致转录下调和果皮颜色丧失。群体基因组分析进一步从人类选择的2494个基因中鉴定出12个标记基因,这些基因在驯化过程中被重塑以增强裂核性状。这些标记基因包括果皮和糊粉层厚度的标记基因Pl1和Dek1;THP9、Sh2、SUS1、Smk10、KW1、O7和NKD1参与蛋白质和淀粉的生物合成;VP5、CCD7和Crti3参与胡萝卜素的生物合成,它们都影响胚乳玻璃体的硬度,而玻璃体是决定爆粒硬度的关键因素。在这些基因中,KW1和O7是对裂粒性能有显著影响的关键基因。这些结果提供了丰富的基因靶点,大大加快了爆米花改良品种的分子育种。
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来源期刊
Plant Biotechnology Journal
Plant Biotechnology Journal 生物-生物工程与应用微生物
CiteScore
20.50
自引率
2.90%
发文量
201
审稿时长
1 months
期刊介绍: Plant Biotechnology Journal aspires to publish original research and insightful reviews of high impact, authored by prominent researchers in applied plant science. The journal places a special emphasis on molecular plant sciences and their practical applications through plant biotechnology. Our goal is to establish a platform for showcasing significant advances in the field, encompassing curiosity-driven studies with potential applications, strategic research in plant biotechnology, scientific analysis of crucial issues for the beneficial utilization of plant sciences, and assessments of the performance of plant biotechnology products in practical applications.
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