Skip to main content
SpringerLink
Log in

Genetic Analysis of Rice Restorer Line Yazhan

  • Original Paper
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

Yazhan is a restorer rice line bred by Jiangxi Tianya Seed Industry Co., LTD, and its hybrid combination has a high yield, excellent rice quality, and strong resistance. In this study, Yazhan, Huazhan, and Zhanhui 15 were used as the experimental materials. Based on agronomic traits, SSR primer screening and second-generation resequencing were conducted to study the genetic basis of Yazhan. The results showed that the plant height of Yazhan was significantly lower than Zhanhui 15, and the yield was not different from the parent lines. The genetic material on chromosome 1, 3, 4, 5, and 10 in the genome of Yazhan were mainly from Zhanhui 15, genetic materials from chromosomes 2, 6, 8, 9, 11, and 12 mainly come from Huazhan, and the chromosomes 1, 5, and 6 had the most variation. In terms of genomic similarity, Yazhan was more similar to the male parent (Huazhan). Yazhan and Huazhan carried the Wxb genotype, while Zhanhui 15 carried the Wxa genotype. The amylose contents of Yazhan and Huazhan were significantly lower than Zhanhui 15. Yazhan and Huazhan carried the Pita blast resistance gene, and Zhanhui 15 carried the Pita susceptibility gene. The results of this study provide a theoretical reference for elucidating the genetic composition of Yazhan and determining the main genetic sources of its important agronomic traits.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Abbreviations

AACC:

American Grain Chemical Association

AC:

Amylose content

BRR:

Brown rice rate

CD:

Chalkiness degree

CMS:

Cytoplasmic male sterility

CS:

Chalkiness size

EPN:

Effective panicle number

FGN:

Filled grain number per panicle

GC:

Gel consistency

HRR:

Head rice rate

LWR:

Length-width ratio

WRR:

White rice rate

PaT:

Pasting temperature

PGWC:

Percentage of grains with chalkiness

PH:

Plant height

PL:

Panicle length

PKV:

Peak viscosity

P/TMS:

Photoperiod/Temperature sensitive genic male sterility

RVA:

Rice starch viscosity characteristic analysis

SS:

Seed setting rate

TCW:

Thermal Cycle for Windows

TGN:

Total grain number per panicle

TGW:

1000-grain weight

YP:

Yield per plant

References

  • Ayres NM, Mcclung AM, Larkin PD et al (1997) Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm. Theor Appl Genet 94:773–781

    Article  CAS  Google Scholar 

  • Babu BK, Meena V, Agarwal V, Agrawal PK (2014) Population structure and genetic diversity analysis of Indian and exotic rice (Oryza sativa L.) accessions using SSR markers. Mol Biol Rep 41:4329–4339

    Article  CAS  Google Scholar 

  • Ball SG, Wal MHBJ, Visser RGF (1998) Progress in understanding the biosynthesis of amylose. Trend Plant Sci 03:462–467

    Article  Google Scholar 

  • Ballini E, Morel JB, Droc G, Price A, Courtois B, Notteghem JL, Tharreau D (2008) A genome-wide meta-analysis of Rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol Plant-Microbe Interact 21:859–868

    Article  CAS  Google Scholar 

  • Brondani C, Rangel P, Borba TC, Vianello R (2003) Transferability of microsatellite and sequence tagged site markers in Oryza species. Hereditas 138:187–192

    Article  Google Scholar 

  • Bryan GT, Wu KS, Farrall L et al (2000) tA single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12:2033–2045

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cai XL, Al E (2010) Aberrant splicing of intron 1 leads to the heterogeneous 5' UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J 14:459–465

    Article  Google Scholar 

  • Cai XL, Liu QQ, Tang SZ, et al (2002) Development of a molecular marker for screening the rice cultivars with intermediate amylose content in Oryza sativa subsp. indica. Acta Photophysiologica Sinica 28:137–144

  • Cao YJ, You SM, Jiang KF et al (2017) Genetic diversity analysis of core rice restorer lines of China and South Asia and Southeat Asia based on yield loci related markers. J Plant Genet Resour 18:396–403

    Google Scholar 

  • Cheng S, Ge H, Wang Z, Hong M (2001) Analysis of influence of Wx intron 1 on gene expression in transgenic rice plant. Acta Photophysiol Sin 05:381–38630

    Google Scholar 

  • Fan CC, Yu XQ, Xing YZ et al (2005) The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet 110:1445–1452

    Article  CAS  Google Scholar 

  • Hu PS, Zhai HQ, Tang SQ, Wan JM (2004) Rapid evaluation of rice cooking and palatability quality by RVA profile. Acta Agron Sin 30:519–524

    Google Scholar 

  • Hu DW, Sheng ZH, Chen W et al (2017) Identification of QTLs associated with high yield of super rice variety Zhongjiazao 17. Acta Agron Sin 43:1434–1447

    Article  Google Scholar 

  • Jia Y, Mcadams SA, Bryan GT, Hershey HP, Valent B (2014) Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. EMBO J 19:4004–4014

    Article  Google Scholar 

  • Kai W, Mingyao L, Hakon H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38:164

    Article  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  Google Scholar 

  • Li YZ, Ma HM, Zhang JL, Wang ZY, Hong MM (1995) Effects of the first intron of rice Waxy gene on the expression of foreign genes in rice and tobacco protoplasts. Plant Sci 108:181–190

    Article  CAS  Google Scholar 

  • Liu HN, Wang SQ, Deng QM et al (2011) Analysis of key genome regions related yield characters of Shuhui527, an elite rice backbone parent. J Agric Biotechnol 19:393–406

    CAS  Google Scholar 

  • Liu J, Yao XY, Liu D et al (2019) Identification of QTL for panicle traits under multiple environments in rice (Oryza sativa L.). Chin J Rice Sci 33:124–134

    Google Scholar 

  • Ma GH, Yuan LP (2015) Hybrid rice achievements, development and prospect in China. J Integr Agric 14:197–205

    Article  Google Scholar 

  • McKenna A, Hanna M, Banks E et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    Article  CAS  Google Scholar 

  • Miah G, Rafii MY, Ismail MR et al (2013) Blast resistance in rice: a review of conventional breeding to molecular approaches. Mol Biol Rep 40:2369–2388

    Article  CAS  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 08:4321–4325

    Article  CAS  Google Scholar 

  • Shi YF, Ying JZ, Wang L, Zhu ZW, Zhuang JY (2005) Screening SSR markers for rice variety identification. Chin J Rice Sci 03:195–201

    Google Scholar 

  • Smith AM, Denyer K, Martin C (1997) The synthesis of the starch granule. Annu Rev Plant Physiol Plant Mol Biol 48:67

    Article  CAS  Google Scholar 

  • Teng B, Zeng R, Wang Y et al (2012) Detection of allelic variation at the Wx locus with single-segment substitution lines in rice (Oryza sativa L.). Mol Breeding 30:583–595

    Article  Google Scholar 

  • Wang F, Cheng FM, Zhong LJ, Sun ZX (2003) Difference of RV A Profile Among Different Early Indica Rice Varieties and Effect of Temperature at Grain Filling Stage on it. Chinese J Rice Sci 17:328–332

  • Wang YY, Zhu YS, Wu FX et al (2009) Genetic diversity analysis with SSR markers for main restore lines of hybrid rice. Mol Plant Breeding 07:279–282

    CAS  Google Scholar 

  • Wang ZY, Zheng FG, Gao JP et al (2010) The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 07:613–62226

    Article  Google Scholar 

  • Wang YY, Cai QH, Liao CJ et al (2017) Grain quality of primal parental lines in hybrid rice breeding. Fujian J Agric Sci 32:242–247

    Google Scholar 

  • Yan C, Zheng J, Duan WJ et al (2019) Locating QTL controlling yield traits in overwintering cultivated rice. Acta Agron Sin 45:522–537

    Article  Google Scholar 

  • Zhang YZ, Luo RJ, Sheng ZH et al (2017) QTL mapping of yield associated traits of Nipponbare ×Zhongjiazao 17 RIL population. Sci Agric Sin 50:3640–3651

    Google Scholar 

  • Zhao YZ, Ni SJ, Zhang Z et al (2017) Analysis of quality character and relationship variation of rice from Liaoning Province. J Plant Genet Resour 18:1039–1045

    Google Scholar 

  • Zhu M, Gu M, Tang S (2007) Correlation analysis of starch RVA profiles and cooking physical-chemical indices of different cultivars lines and DH populations in Japonica rice. Acta Agron Sin 03:411–418

    Google Scholar 

Download references

Funding

This study was financially supported by the National Key Research and Development Program of China (2016YFD0101104), Major project of Jiangxi Provincial Department of Science and Technology (S2016NYZPF0256).

Author information

Authors and Affiliations

  1. Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, (Jiangxi Agricultural University), Ministry of Education/ Jiangxi Province, Nanchang, 330045, Jiangxi, China

    Shuang Li, Yue Sun, Chunlei Wang, Jianmin Bian, Jie Xu, Haohua He & Xiaosong Peng

  2. Jiangxi Tianya Seed Industry Co., LTD, Pingxiang, 337016, Jiangxi, China

    Shuang Li & Qiuping Yu

Authors
  1. Shuang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qiuping Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yue Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chunlei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jianmin Bian
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jie Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Haohua He
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Xiaosong Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiaosong Peng.

Ethics declarations

Conflict of Interest

The authors declared that they have no conflicts of interest to this work. We declare that we do not have any commercial or associative interest that represents a conflict of interest in connection with the work submitted.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Key Message

Based on agronomic traits, SSR primer screening and second-generation resequencing was conducted to study the genetic basis of Yazhan. Genetic basis revealed that the chromosomes 1, 5, and 6 had the most variation in the genome of Yazhan. Yazhan was more similar to the male parent (Huazhan) in genomic similarity. Yazhan and Huazhan carried the Wxb genotype and the Pita blast resistance gene, while Zhanhui 15 carried the Wxa genotype and the Pita susceptibility gene.

Electronic supplementary material

ESM 1

(DOC 443 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, S., Yu, Q., Sun, Y. et al. Genetic Analysis of Rice Restorer Line Yazhan. Plant Mol Biol Rep 38, 394–403 (2020). https://doi.org/10.1007/s11105-020-01201-6

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-020-01201-6

Keywords

Search

Navigation