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首页> 外文期刊>Genomics Insights >Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents:
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Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents:

机译：基于3种高密度单核苷酸多态性和共同父母独立制定的共识图的陆地棉遗传重组的见解：

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High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton (Gossypium hirsutum L., “2n?=?52”). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F2, a recombinant inbred line (RIL), and reciprocal RIL population, from “Phytogen 72” and “Stoneville 474” cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD)1 arisen from the merging of 2 genomes (“A” Old World and “D” New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538?cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the At and Dt subgenomes with 1825 and 1713?cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the Dt subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral At-subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of Gossypium hirsutum. However, the genomic comparisons revealed evidence of additional unconfirmed possible duplications, inversions and translocations, and unbalance SNP sequence homology or SNP sequence/loci genomic dominance, or homeolog loci bias of the upland tetraploid At and Dt subgenomes. The alignments indicated that 364 SNP-associated previously unintegrated scaffolds can be placed in pseudochromosomes of the NBI G hirsutum assembly. This is the first intraspecific SNP genetic linkage consensus map assembled in G hirsutum with a core of reproducible mendelian SNP markers assayed on different populations and it provides further knowledge of chromosome arrangement of genic and nongenic SNPs. Together, the consensus map and RIL populations provide a synergistically useful platform for localizing and identifying agronomically important loci for improvement of the cotton crop.
机译：高密度连锁图对于支持支架和基因序列在染色体上的正确放置以及当代有机研究和遗传改良科学方法的基础至关重要，特别是在具有异常复杂基因组的古多倍体中，例如陆地棉（Gossypium hirsutum L.， “ 2n？=？52”）。分析了三个独立开发的种内高地制图种群，以使用CottonSNP63K阵列生成了3个高密度遗传连锁单核苷酸多态性（SNP）图和共有图。种群由先前报道的F2，重组自交系（RIL）和互为RIL种群组成，分别来自“ Phytogen 72”和“ Stoneville 474”品种。该簇文件提供了7417个基因型SNP标记，导致26个连锁群对应于异源四倍体陆地棉（AD）1的26条染色体（c），这是由两个基因组（“ A”旧世界和“ D”新世界）的合并产生的）。染色体特异重组的模式在所有作图人群中基本一致。高密度遗传共有图谱包括7244个SNP标记，跨度3538？cM，包括3824个SNP仓位，其中1783和2041位于At和Dt亚基因组中，分别具有1825和1713？cM图谱的长度。亚基因组的平均距离几乎相同，这表明由于Dt亚基因组上SNP的数量过多，导致bin数目的亚基因组差异。检查2个亚基因组每个种群内染色体上的预期重组频率或交叉（CO），发现CO也不受这些亚基因组中SNP或SNP bin数目的影响。比较比对分析确定了c02和c03以及c04和c05的历史祖先亚基因组易位。共有图谱SNP序列与陆地棉的NBI装配高度一致。但是，基因组比较显示了其他未确认的可能重复，倒置和易位，以及不平衡的SNP序列同源性或SNP序列/基因组基因优势，或山地四倍体At和Dt亚基因组的同源位点偏倚的证据。比对表明可以将364个与SNP相关的先前未整合的支架放置在NBI Ghirsutum组装体的假染色体中。这是在G hirsutum中组装的第一份种内SNP遗传连锁共有图谱，其核心是在不同种群上测定的可再现孟德尔SNP标记，它提供了有关基因SNP和非基因SNP染色体排列的进一步知识。共有图谱和RIL群体共同提供了一个协同有用的平台，可用于定位和确定农艺上重要的基因座，从而改善棉花作物。

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