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针对多种生物能源高粱基因型的十个新的高质量基因组组装。

Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.

作者信息

Voelker William G, Krishnan Krittika, Chougule Kapeel, Alexander Louie C, Lu Zhenyuan, Olson Andrew, Ware Doreen, Songsomboon Kittikun, Ponce Cristian, Brenton Zachary W, Boatwright J Lucas, Cooper Elizabeth A

机构信息

Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States.

North Carolina Research Campus, Kannapolis, NC, United States.

出版信息

Front Plant Sci. 2023 Jan 4;13:1040909. doi: 10.3389/fpls.2022.1040909. eCollection 2022.

DOI:10.3389/fpls.2022.1040909
PMID:36684744
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9846640/
Abstract

INTRODUCTION

Sorghum ( (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.

METHODS

Expanding on a recently developed mapping population, we generated genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).

RESULTS

We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.

DISCUSSION

These resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.

摘要

引言

高粱（(L.) Moench）是一种在农业和经济上都很重要的主食作物，由于其在边际土地上具有相对较高的生产力，作为生物能源原料具有巨大潜力。为了利用并进一步提升高粱作为可持续生物燃料潜在来源的价值，了解与产量、成分和环境适应性相关的复杂性状的基因组机制至关重要。

方法

在最近开发的一个作图群体的基础上进行拓展，我们为此群体中的10个亲本基因型生成了基因组组装，并鉴定出一套全面的超过2.4万个大结构变异（SVs）和超过1050万个单核苷酸多态性（SNPs）。

结果

我们表明，SVs和非同义SNPs在不同基因类别中富集，强调了在作物物种中进行长读长测序以识别新变异的必要性。此外，我们突出了在与关键生物能源相关表型有已知关联的基因和途径中出现的SVs和SNPs，并描绘了甜高粱和纤维素型高粱基因型之间的遗传差异格局。

讨论

这些资源可整合到高粱目前及未来的作图和性状发现中，以及高粱的众多用途中，包括食品、饲料、生物能源，并且越来越多地作为一种二氧化碳去除机制。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/47612cf95547/fpls-13-1040909-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/c1da346f4a53/fpls-13-1040909-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/da5f12b68e9e/fpls-13-1040909-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/7b821675bdac/fpls-13-1040909-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/d074f749ea1f/fpls-13-1040909-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/221776006055/fpls-13-1040909-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/47612cf95547/fpls-13-1040909-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/c1da346f4a53/fpls-13-1040909-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/da5f12b68e9e/fpls-13-1040909-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/7b821675bdac/fpls-13-1040909-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/d074f749ea1f/fpls-13-1040909-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/221776006055/fpls-13-1040909-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/778c/9846640/47612cf95547/fpls-13-1040909-g006.jpg

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