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. 2023 Jun;73(3):332-342.
doi: 10.1270/jsbbs.23006. Epub 2023 Jun 27.

Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice

Kazufumi Nagata  1 , Yasunori Nonoue  1 , Kazuki Matsubara  1 , Ritsuko Mizobuchi  1 , Nozomi Ono  2 , Taeko Shibaya  1 , Kaworu Ebana  1 , Eri Ogiso-Tanaka  1 , Takanari Tanabata  1 , Kazuhiko Sugimoto  1 , Fumio Taguchi-Shiobara  1 , Jun-Ichi Yonemaru  1 , Yusaku Uga  1 , Atsunori Fukuda  1 , Tadamasa Ueda  1 , Shin-Ichi Yamamoto  1 , Utako Yamanouchi  1 , Toshiyuki Takai  1 , Takashi Ikka  1 , Katsuhiko Kondo  1 , Tomoki Hoshino  1 , Eiji Yamamoto  1 , Shunsuke Adachi  1 , Jian Sun  1 , Noriyuki Kuya  1 , Yuka Kitomi  1 , Ken Iijima  1 , Hideki Nagasaki  1 , Ayahiko Shomura  1 , Tatsumi Mizubayashi  1 , Noriyuki Kitazawa  1 , Kiyosumi Hori  1 , Tsuyu Ando  1 , Toshio Yamamoto  1 , Shuichi Fukuoka  1 , Masahiro Yano  1
Affiliations

Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice

Kazufumi Nagata et al. Breed Sci. 2023 Jun.

Abstract

Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the japonica background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice. Using these materials, we overviewed the chromosomal locations of 1079 putative QTLs for seven agronomic traits and their allelic distribution in Asian cultivated rice through multiple linear regression analysis. The CSSLs will allow the effects of putative QTLs in the highly homogeneous japonica background to be validated.

Keywords: CSSLs; Oryza sativa L.; advanced mapping population; allele mining.

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Figures

Fig. 1.
Fig. 1.
Schematic representation of the development of CSSLs. Marker-assisted selection (MAS) was conducted mainly in backcrossed generations (—), but when target chromosomal regions segregated, it was further conducted in fixing generations (- - -). Proportions of the number of lines are indicated below the three types of lines, which differed in the number of backcrosses.
Fig. 2.
Fig. 2.
Chromosomal distribution of putative QTLs for seven agronomic traits, with number of putative QTLs per megabase on each chromosome.
Fig. 3.
Fig. 3.
Chromosomal locations of putative QTLs for seven agronomic traits found in two or more donors. Chromosome numbers are indicated above; scale to show position on chromosomes is indicated on left. Arrows indicate putative QTLs whose donor alleles ↑ increase or ↓ decrease values. Colors distinguish traits. The numbers on the arrows indicate the number of CSSLs with each putative QTL.
Fig. 4.
Fig. 4.
Locations of putative QTLs for grain length detected on chromosome 2. Codes of CSSLs are indicated above. Gray boxes indicate the most probable regions for putative QTLs based on the final model subjected to multiple linear regression analysis. Open boxes indicate regions that are partly interrupted. Numbers above and below gray boxes show additive effects of donor alleles on grain length in red (positive) or blue (negative). Red dashed rectangles indicate consensus regions (Cons.) among the 12 CSSLs; results are shown as red arrows to the right, together with the numbers of CSSLs that detected each putative QTL. Box on the right shows QTL regions found by Nagata et al. (2015) and the additive effects of the ‘IR64’ allele on grain length. IRK, BC4F2 population developed with ‘Koshihikari’ as the recurrent parent. KSI, BC4F2 population developed with ‘IR64’ as the recurrent parent.
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