Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes.
Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes.
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DOI：
10.1007/s00438-022-01942-x
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发表时间：
2022-11
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--
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通过对混合表型极值的选择性基因分型，我们鉴定了一些控制红三叶草茎伸长时间的位点和候选基因。我们已经确定了控制红三叶草开花前茎伸长时间的候选基因。该性状具有生态和农艺学意义，因为它影响适合性、竞争力、气候适应性、牧草和种子产量以及牧草质量。我们使用池中测序基因分型（池-GBS）对栽培品种莱亚内表型极端个体（早期和晚期伸长）的重复池进行基因分型。在调用和过滤SNPs和GBS位点单倍型多态性后，我们估计等位基因频率，并使用BayeScan搜索两个表型组中具有显著不同等位基因频率的标记，这是一种基于FST的测试，利用重复池，以及基于重复池误差方差的测试。在这三种方法中，BayeScan最不严格，基于误差方差的检验最严格。15个显着的标志物被确定在共同的所有三个测试。侧翼的标记的候选基因包括在春化，自主和光周期调节花的转变，激素调节茎伸长，和细胞生长的潜在作用的基因。这些结果提供了第一个洞察潜在的基因和机制控制过渡到茎伸长多年生豆科植物，这奠定了基础，为进一步的功能研究的遗传决定因素调节这一重要性状。在线版本包含补充材料，可通过10.1007/s 00438 -022-01942-x获得。
Through selective genotyping of pooled phenotypic extremes, we identified a number of loci and candidate genes putatively controlling timing of stem elongation in red clover. We have identified candidate genes controlling the timing of stem elongation prior to flowering in red clover (Trifolium pratense L.). This trait is of ecological and agronomic significance, as it affects fitness, competitivity, climate adaptation, forage and seed yield, and forage quality. We genotyped replicate pools of phenotypically extreme individuals (early and late-elongating) within cultivar Lea using genotyping-by-sequencing in pools (pool-GBS). After calling and filtering SNPs and GBS locus haplotype polymorphisms, we estimated allele frequencies and searched for markers with significantly different allele frequencies in the two phenotypic groups using BayeScan, an FST-based test utilizing replicate pools, and a test based on error variance of replicate pools. Of the three methods, BayeScan was the least stringent, and the error variance-based test the most stringent. Fifteen significant markers were identified in common by all three tests. The candidate genes flanking the markers include genes with potential roles in the vernalization, autonomous, and photoperiod regulation of floral transition, hormonal regulation of stem elongation, and cell growth. These results provide a first insight into the potential genes and mechanisms controlling transition to stem elongation in a perennial legume, which lays a foundation for further functional studies of the genetic determinants regulating this important trait. The online version contains supplementary material available at 10.1007/s00438-022-01942-x.
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影响因子：
5.6
作者：
He, Jiadai;Zhao, Hua;Ma, Haoli
通讯作者：
Ma, Haoli
DOI：
10.1073/pnas.0900689106
发表时间：
2009-08-04
影响因子：
11.1
作者：
Barratt, D. H. Paul;Derbyshire, Paul;Smith, Alison M.
通讯作者：
Smith, Alison M.
DOI：
10.1038/nrm4085
发表时间：
2015-12
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Borges F;Martienssen RA
通讯作者：
Martienssen RA
通过测序进行基因分型，获得群体的全基因组等位基因频率指纹 (GWAFF)。
影响因子：
3.7
作者：
Byrne S;Czaban A;Studer B;Panitz F;Bendixen C;Asp T
通讯作者：
Asp T
影响因子：
3.3
作者：
Foll, Matthieu;Gaggiotti, Oscar
通讯作者：
Gaggiotti, Oscar