{"title":"A large deletion within intron 20 sequence of single-copy <i>PolA1</i> gene as a useful marker for the speciation in <i>Oryza</i> AA-genome species.","authors":"Aung Htut Htet, So Makabe, Hiroko Takahashi, Poku Aduse Samuel, Yo-Ichiro Sato, Ikuo Nakamura","doi":"10.1270/jsbbs.21075","DOIUrl":null,"url":null,"abstract":"<p><p><i>Oryza</i> AA-genome complex comprises five wild species, <i>O. rufipogon</i>, <i>O. barthii</i>, <i>O. longistaminata</i>, <i>O. glumaepatula</i>, and <i>O. meridionalis</i>. Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of <i>PolA1</i>, a single-copy nuclear gene, was short (S-type: 141-142 bp) in <i>O. rufipogon</i>, <i>O. barthii</i>, and <i>O. glumaepatula</i>, while long (L-type: <i>ca.</i> 1.5 kb) introns were apparent in <i>O. longistaminata</i> and <i>O. meridionalis</i>. Because <i>Oryza</i> 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 <i>O. barthii</i> was identical to that of <i>O. longistaminata</i>. As more than 3,470 accessions of <i>O. rufipogon</i> and <i>O. sativa</i> also contained the same intron 20 sequence with <i>O. longistaminata</i> except for single T-nucleotide deletion, which was shared with <i>O. glumaepatuala</i>, the deletion of the T-nucleotide probably occurred in the L-type intron 20 of <i>O. logistaminata</i>. Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of <i>PolA1</i> gene were considered as useful DNA markers to study the evolutionary relationships among <i>Oryza</i> AA-genome species.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":null,"pages":null},"PeriodicalIF":2.0000,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9653197/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Breeding Science","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1270/jsbbs.21075","RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2022/7/12 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"AGRONOMY","Score":null,"Total":0}
引用次数: 0
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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