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SCIENCE CHINA Life Sciences, Volume 62, Issue 4: 507-516(2019) https://doi.org/10.1007/s11427-018-9452-8

Genome-wide dissection of segregation distortion using multiple inter-subspecific crosses in rice

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  • ReceivedOct 1, 2018
  • AcceptedOct 28, 2018
  • PublishedMar 7, 2019

Abstract

Mendelian inheritance can ensure equal segregation of alleles from parents to offspring, which provides fundamental basis for genetics and molecular biology. Segregation distortion (SD) leads to preferential transmission of certain alleles from generation to generation. Such violation of Mendelian genetic principle is often accompanied by reproductive isolation and eventually speciation. Although SD is observed in a wide range of species from plants to animals, genome-wide dissection of such biased transmission of gametes is rare. Using nine inter-subspecific rice crosses, a genome-wide screen for SD loci is performed, which reveals 61 single-locus quantitative trait loci and 194 digenic interactions showing distorted transmission ratio, among which 24 new SD loci are identified. Biased transmission of alleles is observed in all nine crosses, suggesting that SD exists extensively in rice populations. 72.13% distorted regions are repeatedly detected in multiple populations, and the most prevalent SD hotspot that observed in eight populations is mapped to chromosome 3. Xian alleles are transmitted at higher frequencies than geng alleles in inter-subspecific crosses, which change the genetic composition of the rice populations. Epistatic interaction contributes significantly to the deviation of Mendelian segregation at the whole-genome level in rice, which is distinct from that in animals. These results provide an extensive archive for investigating the genetic basis of SD in rice, which have significant implications in understanding the reproductive isolation and formation of inter-subspecific barriers during the evolution.


Funded by

grants from the National Natural Science Foundation of China(31771873)

the National Program for Support of Top-notch Young Professionals.


Acknowledgment

We thank Profs. Yongzhong Xing and Shiping Wang for providing the genotype data of the populations. We also thank Yuan Wang and Xu Li for checking the data. This work was supported by grants from the National Natural Science Foundation of China (31771873 and 30800678), the National Program for Support of Top-notch Young Professionals, and the Fundamental Research Funds for the Central Universities (2662017QD033).


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

SUPPORTING INFORMATION

Table S1ƒ Interacting bin clusters showing significant χ2 independence test values in Nip×9311 and XZ2×ZS97 RIL populations

Table S2ƒSegregation distortion regions detected in nine inter-subspecific populations in rice

The supporting information is available online at http://life.scichina.com and http://link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


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  • Figure 1

    Distribution of single-locus and two-locus SD regions in Nip×9311 and XZ2×ZS97 RIL populations. SD, segregation distortion. Cut off suggests –log10(P) higher than 3 for single-locus regions and 4 for two-locus combinations.

  • Figure 2

    Comparison of single-locus and two-locus SD regions between bi-parental populations with one identical parent. Cut off suggests–log10(P) higher than 3 for single-locus regions and 4 for two-locus combinations. A, Comparison of SD in populations with geng rice Nip. B, Comparison of SD in populations with xian rice ZS97.

  • Figure 3

    QTL mapping of single-locus SD regions in nine inter-subspecific populations in rice. Cut off suggests –log10(P) higher than 3.

  • Table 1   Nine inter-subspecific populations used in this study

    Parent 1 (geng)

    Abbreviation

    Parent 2 (xian)

    Abbreviation

    Population

    Maker

    Type

    Number

    Type

    Number

    Nipponbare

    Nip

    9311

    9311

    RIL

    150

    Binmap

    2,334

    Xizang2

    XZ2

    Zhenshan97

    ZS97

    RIL

    206

    SNP

    3,246

    Nipponbare

    Nip

    Zhenshan97

    ZS97

    F2

    157

    Binmap

    2,668

    Nipponbare

    Nip

    Minghui63

    MH63

    F2

    172

    Binmap

    2,643

    Nanyangzhan

    NYZ

    Chuan7

    C7

    RIL

    81

    SSR

    175

    02428

    02428

    Teqing

    TQ

    RIL

    107

    SSR

    176

    Akitakomachi

    Akit

    Dular

    DL

    F2

    102

    SSR

    188

    Dourado Precoce

    DP

    Sadu-cho

    Sadu

    F2

    140

    SSR

    142

    Mudanjiang2

    MDJ2

    Minghui63

    MH63

    F2

    90

    SSR

    134

  • Table 2   Segregation distortion regions detected in Nip×9311 and XZ2×ZS97 RIL populations

    PopulationP1×P2

    Bin name*

    Chr.**

    Region (bp)

    Observed allele freq

    Chi-square test

    Overlapped locus

    Start

    End

    P1 (0.5)

    P2 (0.5)

    χ² (df=1)

    –Log10(P)

    Locus name

    Reference

    Nip×9311

    Bin22

    1

    2,400,000

    3,500,000

    0.220

    0.780

    48.490

    11.479

    S35

    Kubo et al., 2016b

    Bin272

    1

    42,800,000

    44,000,000

    0.760

    0.240

    39.792

    9.549

    /

    /

    Bin582

    3

    7,500,000

    8,000,000

    0.253

    0.747

    39.027

    9.379

    Sc

    Shen et al., 2017

    Bin620

    3

    12,000,000

    14,400,000

    0.260

    0.740

    34.560

    8.384

    /

    /

    Bin859

    4

    19,300,000

    20,000,000

    0.767

    0.233

    41.886

    10.014

    S9

    Wan et al., 1996; Zhao et al., 2006

    Bin1015

    5

    6,100,000

    7,100,000

    0.707

    0.293

    24.973

    6.236

    /

    /

    Bin1184

    6

    4,900,000

    5,400,000

    0.200

    0.800

    55.577

    13.046

    S5

    Chen et al., 2008; Yang et al., 2012

    Bin1706

    9

    5,400,000

    6,400,000

    0.367

    0.633

    14.694

    3.898

    /

    /

    Bin2155

    12

    500,000

    1,200,000

    0.067

    0.933

    112.667

    25.593

    pf12/qS12

    Song et al., 2005; Zhang et al., 2011

    Bin2231

    12

    11,300,000

    12,500,000

    0.673

    0.327

    15.234

    4.022

    /

    /

    XZ2×ZS97

    SNP20

    1

    1,402,436

    3,042,592

    0.379

    0.621

    15.680

    4.125

    S35

    Kubo et al., 2016b

    SNP60

    1

    6,775,846

    8,375,021

    0.345

    0.655

    19.883

    5.085

    DPL1

    Mizuta et al., 2010

    SNP281

    1

    29,325,880

    32,496,630

    0.379

    0.621

    12.136

    3.306

    /

    /

    SNP402

    2

    1,660,713

    3,481,536

    0.316

    0.684

    30.744

    7.531

    S32

    Li et al., 2007

    SNP482

    2

    11,401,648

    17,200,337

    0.316

    0.684

    28.039

    6.925

    /

    /

    SNP863

    3

    5,200,836

    10,203,488

    0.330

    0.670

    23.786

    5.967

    Sc

    Shen et al., 2017

    SNP922

    3

    12,613,684

    13,308,973

    0.223

    0.777

    63.087

    14.704

    /

    /

    SNP1365

    4

    30,687,479

    33,344,629

    0.354

    0.646

    17.476

    4.536

    /

    /

    SNP2262

    7

    19,605,466

    22,101,586

    0.306

    0.694

    31.068

    7.604

    S30

    Zhu et al., 2005

    SNP2381

    8

    1,622,169

    2,128,278

    0.369

    0.631

    15.373

    4.054

    f8/qSS-8b/spf8

    Wang et al., 1998; Wang et al., 2005; Song et al., 2005

    SNP2555

    8

    27,175,385

    28,112,761

    0.379

    0.621

    12.136

    3.306

    /

    /

    SNP3029

    11

    5,007,401

    9,039,512

    0.354

    0.646

    17.476

    4.536

    S34

    Jing et al., 2007

    SNP3171

    12

    152,441

    1,392,051

    0.228

    0.772

    66.614

    15.481

    pf12/qS12

    Song et al., 2005; Zhang et al., 2011

    SNP3350

    12

    23,891,417

    25,860,695

    0.218

    0.782

    65.320

    15.196

    hsa1

    Kubo et al., 2016a

    *, Bins showing the most significant effect. **, Chromosome. Bold print indicates overlapping SD regions identified in Nip×9311 and XZ2×ZS97 RIL populations.

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