Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms.
Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms.
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DOI：
10.1186/1471-2229-11-146
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发表时间：
2011-10-27
影响因子：
5.3
通讯作者：
Bauer E
中科院分区：
文献类型：
--
作者：
Li Y;Böck A;Haseneyer G;Korzun V;Wilde P;Schön CC;Ankerst DP;Bauer E
霜冻是限制温带谷物产量的重要非生物胁迫。作为最耐霜冻的小粒谷物，黑麦（Secale Greeke L.）是研究耐霜冻（FT）这一具有多基因遗传的复杂性状遗传基础的理想谷物模型。 Using 201 genotypes from five Eastern and Middle European winter rye populations, this study reports a multi-platform candidate gene-based association analysis in rye using 161 single nucleotide polymorphisms (SNPs) and nine insertion-deletion (Indel) polymorphisms previously identified from twelve candidate genes with a putative role in the frost responsive network.在三个不同表型平台（对照、半对照和田间）中对 FT 表型数据进行分析，揭示了所研究植物材料的显着遗传变异。确定了 FT 和候选基因的 SNP/单倍型之间具有统计显着性 (P < 0.05) 的关联。 ScCbf15 中的 2 个 SNP 和 ScCbf12 中的 1 个 SNP 均导致氨基酸交换，并且在所有三个表型平台上均与 FT 显着相关。 SNP 效应大小的分布表示为由单个 SNP 解释的遗传方差的百分比，该分布高度偏向于零，少数 SNP 获得了较大的效应。在14对候选基因之间发现双向上位性。在三个平台中观察到 SNP-FT 关联的经验相关性相对较低到中等，这强调需要进行多层次实验来剖析黑麦基因型和 FT 之间的复杂关联。基于候选基因的关联研究是研究黑麦 FT 遗传基础的有力工具。本研究的结果支持双亲连锁图谱和表达研究的结果，即 Cbf 基因家族在 FT 中发挥重要作用。
Frost is an important abiotic stress that limits cereal production in the temperate zone. As the most frost tolerant small grain cereal, rye (Secale cereale L.) is an ideal cereal model for investigating the genetic basis of frost tolerance (FT), a complex trait with polygenic inheritance. Using 201 genotypes from five Eastern and Middle European winter rye populations, this study reports a multi-platform candidate gene-based association analysis in rye using 161 single nucleotide polymorphisms (SNPs) and nine insertion-deletion (Indel) polymorphisms previously identified from twelve candidate genes with a putative role in the frost responsive network. Phenotypic data analyses of FT in three different phenotyping platforms, controlled, semi-controlled and field, revealed significant genetic variations in the plant material under study. Statistically significant (P < 0.05) associations between FT and SNPs/haplotypes of candidate genes were identified. Two SNPs in ScCbf15 and one in ScCbf12, all leading to amino acid exchanges, were significantly associated with FT over all three phenotyping platforms. Distribution of SNP effect sizes expressed as percentage of the genetic variance explained by individual SNPs was highly skewed towards zero with a few SNPs obtaining large effects. Two-way epistasis was found between 14 pairs of candidate genes. Relatively low to medium empirical correlations of SNP-FT associations were observed across the three platforms underlining the need for multi-level experimentation for dissecting complex associations between genotypes and FT in rye. Candidate gene based-association studies are a powerful tool for investigating the genetic basis of FT in rye. Results of this study support the findings of bi-parental linkage mapping and expression studies that the Cbf gene family plays an essential role in FT.
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影响因子：
5.4
作者：
GALIBA, G;QUARRIE, SA;SNAPE, JW
通讯作者：
SNAPE, JW
影响因子：
4.9
作者：
Badawi, Mohamed;Reddy, Yedulla Venkat;Houde, Mario
通讯作者：
Houde, Mario
影响因子：
2.3
作者：
FOWLER, DB;GUSTA, LV;TYLER, NJ
通讯作者：
TYLER, NJ
DOI：
10.1073/pnas.0406069101
发表时间：
2004-10-19
影响因子：
11.1
作者：
Cook, D;Fowler, S;Thomashow, MF
通讯作者：
Thomashow, MF
影响因子：
5.4
作者：
Alm, Vibeke;Busso, Carlos S.;Rognli, Odd Arne
通讯作者：
Rognli, Odd Arne