Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China.
College of Horticulture, Sichuan Agricultural University, Chengdu, China.
BMC Plant Biol. 2019 Jul 10;19(1):303. doi: 10.1186/s12870-019-1915-7.
Polyploidy and hybridization are ubiquitous in Rubus L., a large and taxonomically challenging genus. Chinese Rubus are mainly concentrated into two major sections, the diploid Idaeobatus and the polyploid Malachobatus. However, it remains unclear to be auto- or allo- polyploid origin of polyploids in Rubus. We investigated the homoeologs and the structure of the GBSSI-1 (granule-bound starch synthase I) gene in 140 Rubus individuals representing 102 taxa in 17 (out of the total 24) subsections of 7 (total of 12) sections at different ploidy levels.
Based on the gene structure and sequence divergence, we defined three gene variants, GBSSI-1a, GBSSI-1b, and GBSSI-1c. When compared with GBSSI-1a, both GBSSI-1b and GBSSI-1c have a shorter fourth intron, and GBSSI-1c had an additional deletion in the fifth intron. For diploids, either GBSSI-1a or GBSSI-1b was detected in 56 taxa consisting of 82 individuals from sect. Idaeobatus, while both alleles existed in R. pentagonus and R. peltatus. Both homoeologs GBSSI-1a and GBSSI-1b were identified in 39 taxa (48 individuals) of Malachobatus polyploids. They were also observed in two sect. Dalibardastrum taxa, in one sect. Chamaebatus taxon, and in three taxa from sect. Cylactis. Interestingly, all three homoeologs were observed in the three tetraploid taxa. Phylogenetic trees and networks suggested two clades (I and II), corresponding to GBSSI-1a, and GBSSI-1b/1c sequences, respectively. GBSSI-1 homoeologs from the same polyploid individual were resolved in different well-supported clades, and some of these homoelogs were more closely related to homoelogs in other species than they were to each other. This implied that the homoeologs of these polyploids were donated by different ancestral taxa, indicating their allopolyploid origin. Two kinds of diploids hybridized to form most allotetraploid species. The early-divergent diploid species with GBSSI-1a or -1b emerged before polyploid formation in the evolutionary history of Rubus.
This study provided new insights into allopolyploid origin and evolution from diploid to polyploid within the genus Rubus at the molecular phylogenetic level, consistent with the taxonomic treatment by Yü et al. and Lu.
多倍体和杂交在Rubus L.中普遍存在，Rubus L.是一个大型且分类具有挑战性的属。中国悬钩子主要集中在两个主要的分类群中，二倍体 Idaeobatus 和多倍体 Malachobatus。然而，Rubus 中多倍体的多倍体起源是自交还是异交仍然不清楚。我们研究了 140 个悬钩子个体的同系物和 GBSSI-1（颗粒结合淀粉合成酶 I）基因的结构，这些个体代表了 17 个亚科（总共 24 个）中的 102 个分类群，在不同的倍性水平下，来自 7 个科（总共 12 个）中的 3 个科。
基于基因结构和序列差异，我们定义了三个基因变体，GBSSI-1a、GBSSI-1b 和 GBSSI-1c。与 GBSSI-1a 相比，GBSSI-1b 和 GBSSI-1c 都具有较短的第四内含子，而 GBSSI-1c 在第五内含子中还有一个额外的缺失。对于二倍体，在来自 Idaeobatus 科的 56 个分类群（由 82 个个体组成）中检测到要么是 GBSSI-1a 要么是 GBSSI-1b，而在 R. pentagonus 和 R. peltatus 中则存在这两个等位基因。在 Malachobatus 多倍体的 39 个分类群（48 个个体）中都鉴定出了同源物 GBSSI-1a 和 GBSSI-1b。它们也在两个 Dalibardastrum 分类群、一个 Chamaebatus 分类群和三个来自 Cylactis 分类群的分类群中被观察到。有趣的是，所有三个同源物都在三个四倍体分类群中被观察到。系统发育树和网络表明存在两个分支（I 和 II），分别对应于 GBSSI-1a 和 GBSSI-1b/1c 序列。来自同一多倍体个体的 GBSSI-1 同源物在不同的支持良好的分支中被解析，其中一些同源物与其他物种的同源物比彼此之间的关系更密切。这表明这些多倍体的同源物是由不同的祖先分类群捐赠的，表明它们是异源多倍体的起源。两种二倍体杂交形成了大多数异源四倍体物种。在 Rubus 的进化历史中，在多倍体形成之前，具有 GBSSI-1a 或 -1b 的早期分化的二倍体物种出现了。
本研究从分子系统发育水平上为 Rubus 属内从二倍体到多倍体的异源多倍体起源和进化提供了新的见解，与 Yü 等人和 Lu 的分类学处理一致。
