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A BAC physical map of aus rice cultivar ‘ K asalath’, and the map‐based genomic sequence of ‘ K asalath’ chromosome 1
Author(s) -
Kanamori Hiroyuki,
Fujisawa Masaki,
Katagiri Satoshi,
Oono Youko,
Fujisawa Hiroko,
Karasawa Wataru,
Kurita Kanako,
Sasaki Harumi,
Mori Satomi,
Hamada Masao,
Mukai Yoshiyuki,
Yazawa Takayuki,
Mizuno Hiroshi,
Namiki Nobukazu,
Sasaki Takuji,
Katayose Yuichi,
Matsumoto Takashi,
Wu Jianzhong
Publication year - 2013
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12317
Subject(s) - indel , genetics , biology , bacterial artificial chromosome , chromosome , genome , gene , chromosome regions , single nucleotide polymorphism , genotype
Summary Comparative analysis using available genomic resources within closely related species is an effective way to investigate genomic sequence and structural diversity. Rice ( O ryza sativa L .) has undergone significant physiological and morphological changes during its domestication and local adaptation. We present a complete bacterial artificial chromosome ( BAC ) physical map for the aus rice cultivar ‘ K asalath’, which covers 90% of the sequence of temperate japonica rice cultivar ‘ N ipponbare’. Examination of physical distances between computational and experimental measurements of ‘ K asalath’ BAC insert size revealed the presence of more than 500 genomic regions that appear to have significant chromosome structural changes between the two cultivars. In particular, a genomic region on the long arm of ‘ K asalath’ chromosome 11 carrying a disease‐resistance gene cluster was greatly expanded relative to the ‘Nipponbare’ genome. We also decoded 41.37 Mb of high‐quality genomic sequence from ‘Kasalath’ chromosome 1. Extensive comparisons of chromosome 1 between ‘Kasalath’ and ‘Nipponbare’ led to the discovery of 317 843 single‐nucleotide polymorphisms ( SNP s) and 66 331 insertion/deletion (indel) sites. Nearly two‐thirds of the expressed genes on rice chromosome 1 carried natural variations involving SNP s and/or indels that resulted in substitutions, insertions or deletions of amino acids in one cultivar relative to the other. We also observed gain and loss of genes caused by large indels. This study provides an important framework and an invaluable dataset for further understanding of the molecular mechanisms underlying the evolution and functions of the rice genome.

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