A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family.
A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family.
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DOI：
10.1371/journal.pone.0130890
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Fincher GB
中科院分区：
文献类型：
--
作者：
Houston K;Burton RA;Sznajder B;Rafalski AJ;Dhugga KS;Mather DE;Taylor J;Steffenson BJ;Waugh R;Fincher GB
纤维素是高等植物细胞壁的基本重要组分。它提供了一个支架，允许植物的发育和生长以有序的方式发生。纤维素还提供机械强度，这对于正常发育和使植物能够承受非生物和生物胁迫都是至关重要的。我们对288份二棱和288份六棱春型大麦种质的秆中纤维素浓度进行了定量分析，这些大麦种质是美国农业部资助的大麦协调农业项目（CAP）计划的一部分。当这些加入的人口结构进行了分析，我们确定了六个不同的人口，其中四个，我们认为是由足够数量的加入适合全基因组关联研究（GWAS）。这些品系已经用3072个SNP进行了基因分型，因此我们将性状和遗传数据结合起来进行GWAS。该分析使我们能够确定基因组中包含分子标记和纤维素浓度数据之间显著关联的区域，包括在多个群体中交叉验证的一个区域。为了识别候选基因，我们组装了这些区域的基因内容，并使用这些内容来查询基于RNA-seq的综合基因表达图谱。这为我们提供了多个组织的基因注释和相关表达数据，使我们能够制定出调节纤维素生物合成的候选基因的支持列表。我们的分析确定的几个区域含有在一系列组织和发育阶段与纤维素合成酶A（HvCesA）共表达的基因。这些基因参与初生和次生细胞壁发育。此外，先前通过生物化学方法与纤维素合成相关的基因，如HvCOBRA，一种功能未知的基因，也与相关组中的纤维素水平相关。我们的分析提供了新的见解基因，有助于纤维素含量的谷物秆和更好地了解它们之间的相互作用。
Cellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two – rowed and 288 six – rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with CELLULOSE SYNTHASE A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the genes that contribute to cellulose content in cereal culms and to a greater understanding of the interactions between them.
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影响因子：
7.4
作者：
Burton, RA;Shirley, NJ;Fincher, GB
通讯作者：
Fincher, GB
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
7.4
作者：
Burton, Rachel A.;Ma, Gang;Fincher, Geoffrey B.
通讯作者：
Fincher, Geoffrey B.
DOI：
10.1073/pnas.0608580104
发表时间：
2007-01-23
影响因子：
11.1
作者：
Komatsuda, Takao;Pourkheirandish, Mohammad;Yano, Masahiro
通讯作者：
Yano, Masahiro
影响因子：
1.1
作者：
Earl, Dent A.;vonHoldt, Bridgett M.
通讯作者：
vonHoldt, Bridgett M.