A large deletion within intron 20 sequence of single-copy PolA1 gene as a useful marker for the speciation in Oryza AA-genome species.

IF 2 4区 农林科学 Q2 AGRONOMY Breeding Science Pub Date : 2022-06-01 Epub Date: 2022-07-12 DOI:10.1270/jsbbs.21075
Aung Htut Htet, So Makabe, Hiroko Takahashi, Poku Aduse Samuel, Yo-Ichiro Sato, Ikuo Nakamura
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Abstract

Oryza AA-genome complex comprises five wild species, O. rufipogon, O. barthii, O. longistaminata, O. glumaepatula, and O. meridionalis. Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of PolA1, a single-copy nuclear gene, was short (S-type: 141-142 bp) in O. rufipogon, O. barthii, and O. glumaepatula, while long (L-type: ca. 1.5 kb) introns were apparent in O. longistaminata and O. meridionalis. Because Oryza species containing BB, CC, EE, FF, and GG genome showed L-type introns, the S-type intron was probably derived from the L-type intron by the deletion of a 1.4 kb fragment through intramolecular homologous recombination between two tandem TTTTGC repeats. Excluding the large deletion sequence, intron 20 sequence of O. barthii was identical to that of O. longistaminata. As more than 3,470 accessions of O. rufipogon and O. sativa also contained the same intron 20 sequence with O. longistaminata except for single T-nucleotide deletion, which was shared with O. glumaepatuala, the deletion of the T-nucleotide probably occurred in the L-type intron 20 of O. logistaminata. Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of PolA1 gene were considered as useful DNA markers to study the evolutionary relationships among Oryza AA-genome species.

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单拷贝PolA1基因内含子20序列的大缺失作为水稻aa基因组物种物种形成的有用标记。
Oryza aa基因组复合体包括5个野生物种:O. rufipogon、O. barthii、O. longistaminata、O. glumaepatula和O. meridionalis。这五种野生物种之间的进化关系一直存在争议和不确定性。结果表明,单拷贝核基因PolA1的内含子20在O. rufipogon、O. barthii和O. glumaepatula中较短(s型:141 ~ 142 bp),而在O. longistaminata和O. meridionalis中较长(l型:约1.5 kb)。由于含有BB, CC, EE, FF和GG基因组的Oryza物种显示l型内含子,因此s型内含子可能是通过两个串联TTTTGC重复序列之间的分子内同源重组缺失1.4 kb片段而来源于l型内含子。除大缺失序列外,O. barthii内含子20序列与O. longistaminata完全相同。由于除单个t核苷酸缺失外,有3470多份褐花蓟马和黄花蓟马含有与长叶蓟马相同的内含子20序列,因此t核苷酸的缺失可能发生在长叶蓟马的l型内含子20上。PolA1基因内含子20中1.4 kb的大片段缺失和单个t核苷酸缺失被认为是研究水稻aa基因组种间进化关系的有用DNA标记。
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来源期刊
Breeding Science
Breeding Science 农林科学-农艺学
CiteScore
4.90
自引率
4.20%
发文量
37
审稿时长
1.5 months
期刊介绍: Breeding Science is published by the Japanese Society of Breeding. Breeding Science publishes research papers, notes and reviews related to breeding. Research Papers are standard original articles. Notes report new cultivars, breeding lines, germplasms, genetic stocks, mapping populations, database, software, and techniques significant and useful for breeding. Reviews summarize recent and historical events related breeding. Manuscripts should be submitted by corresponding author. Corresponding author must have obtained permission from all authors prior to submission. Correspondence, proofs, and charges of excess page and color figures should be handled by the corresponding author.
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