Molecular Breeding

, 39:51 | Cite as

Genetic characterization of the chromosome single-segment substitution lines of O. glumaepatula and O. barthii and identification of QTLs for yield-related traits

  • Hanwei Zhao
  • Lingling Sun
  • Tianyi Xiong
  • Zhangqiang Wang
  • Yu Liao
  • Tuo Zou
  • Mingmin Zheng
  • Zhe Zhang
  • Xiaoping Pan
  • Ning He
  • Guiquan Zhang
  • Haitao Zhu
  • Ziqiang Liu
  • Ping He
  • Xuelin FuEmail author


Oryza glumaepatula and Oryza barthii are AA-genome wild species in Oryza genus. In order to effectively mine and transfer beneficial genes from these wild species in genome-wide by distant hybridization, in the present study, the chromosome single-segment substitution lines (SSSLs) were developed using O. glumaepatula and O. barthii as donors and elite indica cultivar, HJX74, as a recipient. A total of 168 homozygous SSSLs of O. glumaepatula (GLU-SSSLs) and 95 homozygous SSSLs of O. barthii (BAR-SSSLs) were developed. In 168 GLU-SSSLs and 95 BAR-SSSLs, the total lengths of the substituted segments distributing on 12 chromosomes were 3636.35 cM and 1731.65 cM, respectively. Accordingly, the mean length of each substituted segment was 21.64 cM in GLU-SSSLs and 18.23 cM in BAR-SSSLs. The total coverage lengths of the substituted segments on rice genome were 80.15% in GLU-SSSLs and 54.67% in BAR-SSSLs. To evaluate the utilization potential of these SSSLs, four yield-related traits, heading date, plant height, seed-setting rate, and 1000-grain weight, were investigated in the SSSLs over two seasons. Significant variations of the traits were observed among the SSSLs. At P ≤ 0.05 level, a sum of 28 stable QTLs in GLU-SSSLs and 53 in BAR-SSSLs were identified. Among them, the additive effects of 12 QTLs contributed averagely more than 10% for phenotypic variations, viz., qPHg1-2, qGWTg9-2, qHDb1-1, qPHb1-2, qPHb1-3, qPHb7-1, qPHb7-2, qPHb8-1, qPHb10-1, qPHb12-2, qSSb7-1, and qSSb10-2. Nine pairs of QTLs in the two donors were comparatively mapped on chromosomes 1, 5, and 10, which means the same QTLs or alleles existing in O. glumaepatula and O. barthii have been detected and transferred to SSSLs. Besides, qGWTg1-1, qGWTg4-1, and qGWTb1-1 have shown positive additive effects, implying alleles from the two wild donors of these QTLs have the potential in increasing 1000-grain weight in SSSLs. The SSSLs library of the wild species is a valuable resource for rice germplasm innovation and breeding.


O. glumaepatula O. barthii Single-segment substitution lines (SSSLs) Genetic characterization QTLs identification 



We thank Liping Peng, Kang Sun, and Rouxian Wu for the assistance in the preliminary work of polymorphic marker selection and hybridization. The accessions of O. glumaepatula and O. barthii were provided by IRRI.

Funding information

This work was supported by Guangzhou Science and Technology Program Key Project (201804020086), the National Natural Science Foundation of China (31671762, 31571483), and the Science and Technology Project of Guangdong Province (2015A030302067).

Supplementary material

11032_2019_960_MOESM1_ESM.doc (84 kb)
ESM 1 (DOC 84 kb)
11032_2019_960_MOESM2_ESM.docx (37 kb)
ESM 2 (DOCX 36 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Hanwei Zhao
    • 1
  • Lingling Sun
    • 1
  • Tianyi Xiong
    • 1
  • Zhangqiang Wang
    • 1
  • Yu Liao
    • 1
  • Tuo Zou
    • 1
  • Mingmin Zheng
    • 1
  • Zhe Zhang
    • 1
  • Xiaoping Pan
    • 1
  • Ning He
    • 1
  • Guiquan Zhang
    • 1
  • Haitao Zhu
    • 1
  • Ziqiang Liu
    • 1
  • Ping He
    • 2
  • Xuelin Fu
    • 1
    Email author
  1. 1.Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
  2. 2.College of Life SciencesSouth China Agricultural UniversityGuangzhouChina

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