Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region

Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6×) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6×) was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase.多倍体化是植物物种形成的核心机制之一。在大麦属（Hordeum）内，约半数类群为多倍体。针对二倍体物种，学界已构建了较为完善的系统发育关系假说，但针对该属多倍体（四倍体、六倍体）的相关研究信息仍较为有限。本研究基于低拷贝核标记区域TOPO6，对341份大麦属个体及8份外类群物种展开分析，以解析全部33个二倍体和多倍体大麦属物种间的亲缘关系。PCR扩增产物可直接测序或克隆测序，每个个体平均纳入12个克隆序列用于系统发育分析。多数二倍体大麦属物种的TOPO6位点大概率为单拷贝。多倍体个体中检出的多数序列在系统发育树上与二倍体物种的同源序列聚类，因此可据此鉴定多倍体的亲本类群。仅在多倍体类群中发现的4组序列，被视为曾参与异源多倍化演化的已灭绝二倍体类群的演化痕迹。本分析明确了3个参与该属美洲多倍体演化的关键类群：（i）除1个美洲四倍体物种外，其余所有美洲四倍体均携带1份来自中亚二倍体H. roshevitzii的TOPO6拷贝，另一份拷贝则与不同美洲二倍体物种聚类；（ii）所有新世界六倍体物种均携带1份与H. californicum近缘的已灭绝类群的拷贝，且均拥有四倍体H. jubatum的TOPO6序列模式，同时各额外携带1份来自不同美洲二倍体的拷贝；（iii）四倍体H. bulbosum为同源多倍体，而此前被认为是同源多倍体的H. brevisubulatum（四倍体、六倍体），在其大部分分布区内被鉴定为异源多倍体。与使用Taq DNA聚合酶相比，在PCR中使用校正型DNA聚合酶可降低多倍体样本中嵌合序列的占比。