■简单序列重复(SSR),也被称为微卫星,是动物和植物中至关重要的分子标记。尽管以前对SSR进行了广泛的研究,芸苔属作物微卫星标记的开发仍然有限且效率低下。
■Krait软件用于通过全基因组和标记开发来识别微卫星,该标记基于U三角形中三种最近测序的芸苔属作物的基本物种(芸苔属,B.nigra和B.oleracea),以及三个异源四倍体(B.juncea,B.napus和B.carinata)使用公共数据库。随后,引物和微卫星的特征,它们中的大多数相应地设计在每个染色体的六个芸苔属物种,并确定了它们的物理位置,并进行了引物的交叉转移。此外,筛选出B基因组特异性SSR标记。
■从U型作物三角形内的芸苔属作物的全基因组序列中鉴定出了79341、92089、125443、173964、173604和222160个SSR基因座,B.rapa(AA),B.nigra(BB),B.麦片(CC),B.napus(AACC),B.juncea(AABB)andB.carinata(BBCC),分别。比较3个亚基因组AA中3个同源四倍体SSR基因座的数量分布,BB和CC,结果表明,与基本二倍体相比,异源四倍体物种基因组中SSR基因座的数量显着减少。此外,我们将基本物种与相应的品种进行了比较,并发现异源四倍体与其相应的基本物种之间的微卫星特征非常相似或几乎相同。随后,40个SSR引物中的每一个都被用于研究B.rapa的多态性潜力(85.27%),B.nigra(81.33%)和B.oleracea(73.45%),并且发现B.rapa在U的三角形中的基本物种之间具有较高的交叉转移率。同时,B基因组特异性SSR标记,获得了具有(AAGGA)3序列特征的BniSSR23228,它位于B3染色体,总长度为97bp。
■在这项研究中,结果表明,在基本芸苔属物种及其异源四倍体对应物的分化过程中,分布模式可能是高度保守的。我们的数据表明,异源四倍体化过程导致三个亚基因组AA中SSR基因座的显着减少,BB和CC原因可能是在基本二倍体物种进化为异源四倍体的过程中,部分基因主导的染色体同源重组和重排。本研究为今后甘蓝型油菜物种亲缘关系的基因组学和遗传学研究提供了基础。
UNASSIGNED: Simple sequence repeats (SSR), also known as microsatellites, are crucial molecular markers in both animals and plants. Despite extensive previous research on SSRs, the development of
microsatellite markers in Brassica crops remains limited and inefficient.
UNASSIGNED: Krait software was used to identify microsatellites by genome-wide and marker development based on three recently sequenced basic species of Brassica crops in the triangle of U (Brassica rapa, B. nigra and B. oleracea), as well as three allotetraploids (B. juncea, B. napus and B. carinata) using public databases. Subsequently, the primers and the characteristics of microsatellites for most of them were accordingly designed on each chromosome of each of the six Brassica species, and their physical locations were identified,and the cross-transferability of primers have been carried out. In addition, a B-genome specific SSR marker was screened out.
UNASSIGNED: A total of 79341, 92089, 125443, 173964, 173604, and 222160 SSR loci have been identified from the whole genome sequences of Brassica crops within the triangle of U crops, B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. napus (AACC), B. juncea (AABB) and B. carinata (BBCC), respectively. Comparing the number distribution of the three allotetraploid SSR loci in the three subgenomes AA, BB and CC, results indicate that the allotetraploid species have significant reduction in the number of SSR loci in the genome compared with their basic diploid counterparts. Moreover, we compared the basic species with their corresponding varieties, and found that the
microsatellite characters between the allotetraploids and their corresponding basic species were very similar or almost identical. Subsequently, each of the 40 SSR primers was employed to investigate the polymorphism potential of B. rapa (85.27%), B. nigra (81.33%) and B. oleracea (73.45%), and B. rapa was found to have a higher cross-transfer rate among the basic species in the triangle of U. Meanwhile, a B-genome specific SSR marker, BniSSR23228 possessing the (AAGGA)3 sequence characteristics was obtained, and it located in chromosome B3 with a total length of 97 bp.
UNASSIGNED: In this study, results suggest that the pattern of distribution may be highly conserved during the differentiation of basic Brassica species and their allotetraploid counterparts. Our data indicated that the allotetraploidization process resulted in a significant reduction in SSR loci in the three subgenomes AA, BB and CC. The reasons may be partial gene dominated chromosomal homologous recombination and rearrangement during the evolution of basic diploid species into allotetraploids. This study provides a basis for future genomics and genetic research on the relatedness of Brassica species.