高密度连锁图谱对于支持支架和基因序列在染色体上的正确放置至关重要，也是当代生物研究和遗传改良科学方法的基础。特别是在基因组异常复杂的古多倍体中，例如，陆地棉(陆地棉，\"2n=52\")。使用CottonSNP63K阵列分析了三个独立开发的种内陆域作图种群，以生成3个高密度遗传连锁单核苷酸多态性（SNP）图谱和共识图谱。种群由先前报道的重组自交系F2（RIL）组成，和倒数RIL人口，来自“Phytogen72”和“Stoneville474”品种。集群文件提供了7417个基因型SNP标记，产生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），来自2个基因组的合并（“A”旧世界和“D”新世界）。染色体特异性重组的模式在作图群体中基本一致。高密度遗传共识图谱包括7244个SNP标记，跨越3538cM，包含3824个SNP箱，其中1783和2041位于At和Dt亚基因组中，具有1825和1713cM图谱长度，分别。亚基因组平均距离几乎相同，这表明由于Dt亚基因组上的高数量的SNP，导致了bin数量的亚基因组差异。对2个亚基因组的每个群体内的染色体上的预期重组频率或交叉(CO)的检查显示,CO也不受这些亚基因组中的SNP或SNPbin数目的影响。比较比对分析鉴定了c02和c03以及c04和c05的历史祖先At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。然而,基因组比较揭示了其他未经证实的可能重复的证据，倒置和易位，和不平衡的SNP序列同源性或SNP序列/基因座基因组优势，或陆地四倍体At和Dt亚基因组的同源位点偏向。比对表明，可以将364个SNP相关的先前未整合的支架放置在NBIG陆生组件的假染色体中。这是在Ghirsutum中组装的第一个种内SNP遗传连锁共识图，具有在不同种群上测定的可重复的孟德尔SNP标记的核心，它提供了对基因和非基因SNP染色体排列的进一步了解。一起,共识图和RIL种群为定位和识别农业上重要的基因座以改善棉花作物提供了协同有用的平台。
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.
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