Integrative multi-omic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves.

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY
Meng Lin, Harel Bacher, Richard Bourgault, Pengfei Qiao, Susanne Matschi, Miguel F Vasquez, Marc Mohammadi, Sarah van Boerdonk, Michael J Scanlon, Laurie G Smith, Isabel Molina, Michael A Gore
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Abstract

Studying the genetic basis of leaf wax composition and its correlation with leaf cuticular conductance (gc) is crucial for improving crop productivity. The leaf cuticle, which comprises a cutin matrix and various waxes, functions as an extracellular hydrophobic layer, protecting against water loss upon stomatal closure. To address the limited understanding of genes associated with the natural variation of adult leaf cuticular waxes and their connection to gc, we conducted statistical genetic analyses using leaf transcriptomic, metabolomic, and physiological data sets collected from a maize (Zea mays L.) panel of ∼300 inbred lines. Through a random forest analysis with 60 cuticular wax traits, it was shown that high molecular weight wax esters play an important role in predicting gc. Integrating results from genome-wide and transcriptome-wide studies (GWAS and TWAS) via a Fisher's combined test revealed 231 candidate genes detected by all three association tests. Among these, 11 genes exhibit known or predicted roles in cuticle-related processes. Throughout the genome, multiple hotspots consisting of GWAS signals for several traits from one or more wax classes were discovered, identifying four additional plausible candidate genes and providing insights into the genetic basis of correlated wax traits. Establishing a partially shared genetic architecture, we identified 35 genes for both gc and at least one wax trait, with four considered plausible candidates. Our study enhances the understanding of how adult leaf cuticle wax composition relates to gc and implicates both known and novel candidate genes as potential targets for optimizing productivity in maize.

多组学综合分析确定了玉米成株叶片中与角质蜡生物发生相关的基因。
研究叶蜡成分的遗传基础及其与叶片角质层传导率(gc)的相关性对于提高作物产量至关重要。叶片角质层由角质蛋白基质和各种蜡质组成,起着细胞外疏水层的作用,防止气孔关闭时水分流失。为了解决对与成叶角质层蜡自然变异有关的基因及其与气孔的关系了解有限的问题,我们利用从玉米(Zea mays L.)300 个近交系中收集的叶片转录组、代谢组和生理数据集进行了统计遗传分析。通过对 60 个角质蜡性状进行随机森林分析,结果表明高分子量蜡酯在预测 gc 方面起着重要作用。通过费雪综合测试,整合了全基因组和全转录组研究(GWAS 和 TWAS)的结果,发现了 231 个通过所有三种关联测试检测到的候选基因。其中,11 个基因在角质层相关过程中显示出已知或预测的作用。在整个基因组中,发现了由一个或多个蜡类的多个性状的 GWAS 信号组成的多个热点,确定了另外 4 个可信的候选基因,为相关蜡类性状的遗传基础提供了深入的见解。通过建立一个部分共享的遗传结构,我们确定了 35 个基因同时与 gc 和至少一个蜡性状相关,其中有四个基因被认为是可信的候选基因。我们的研究加深了人们对成株叶片角质层蜡质组成与gc关系的理解,并将已知和新的候选基因作为优化玉米生产力的潜在目标。
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来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
期刊介绍: G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.
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