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作物学报 ›› 2022, Vol. 48 ›› Issue (10): 2483-2493.doi: 10.3724/SP.J.1006.2022.12067

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于SLAF标签测序分析广东省栽培稻种质资源的遗传结构及演化关系

孙炳蕊(), 潘大建, 李晨, 江立群, 张静, 吕树伟, 刘清, 毛兴学, 陈文丰(), 范芝兰()   

  1. 广东省农业科学院水稻研究所 / 广东省水稻育种新技术重点实验室 / 广东省水稻工程实验室, 广东广州 510640
  • 收稿日期:2021-09-16 接受日期:2022-02-25 出版日期:2022-10-12 网络出版日期:2022-03-15
  • 通讯作者: 陈文丰,范芝兰
  • 作者简介:第一作者联系方式: E-mail: sunbingrui2003@163.com
  • 基金资助:
    广东省重点领域研发计划项目(2020B020219004);广东省基础与应用基础研究基金项目(2021A1515011226);广东省广州市国家野生稻种质资源圃项目(粤发改农经[2021]272号);广东省农业科学院水稻研究所“优谷计划”(所长基金)项目(2021YG02);广东重点实验室(2020B1212060047);广东省重点领域研发计划项目(2020B020219004)

Genetic structure and evolutionary relationship for cultivated rice resources from Guangdong province based on SLAF tag sequencing

SUN Bing-Rui(), PAN Da-Jian, LI Chen, JIANG Li-Qun, ZHANG Jing, LYU Shu-Wei, LIU Qing, MAO Xing-Xue, CHEN Wen-Feng(), FAN Zhi-Lan()   

  1. Rice Research Institute, Guangdong Academy of Agricultural Sciences / Guang Key Laboratory of New Technology in Rice Breeding / Guangdong Rice Engineering Laboratory, Guangdong 510640, Guangzhou, China
  • Received:2021-09-16 Accepted:2022-02-25 Published:2022-10-12 Published online:2022-03-15
  • Contact: CHEN Wen-Feng,FAN Zhi-Lan
  • Supported by:
    Key-Area Research and Development Program of Guangdong Province(2020B020219004);Basic and Applied Basic Research Fund of Guangdong Province(2021A1515011226);National Wild Rice Germplasm Resource Nursery (Guangzhou,Guangdong) Project ([2021]272);“You-Gu Plan” (Director’s Fund) of Rice Research Institute, Guangdong Academy of Agricultural Science(2021YG02);Key Laboratory of Guangdong Province(2020B1212060047);Key-Area Research and Development Program of Guangdong Province(2020B020219004)

摘要:

自水稻矮化育种成功以来, 广东的水稻品种在国内的水稻育种中发挥了重要作用。国家“十四五”规划明确提出了我国种业自主创新将以提升核心种源竞争力为目标, 着力加强种质资源保护利用。本研究利用开发的10,610个多态性SLAF标签, 对98份广东省不同时期育成的代表性品种和地方稻种, 开展遗传演化、群体遗传结构及主成分分析, 发现43份老品种和5份地方稻种的遗传基础较宽, 而50份近期育成的新品种的遗传基础较窄; 遗传演化和系谱分析发现, 老品种大多数含有广场13、南特号、矮仔占、塘埔矮和竹印2号的血缘, 而新品种大多含有IR系列品种、粳籼677、广场矮、中籼3588的血缘。这表明自20世纪90年代以来重视了外引材料的利用, 但忽视了对本地优良种质资源的利用。这可能与20世纪70年代三系杂交稻的兴起有关。因此, 为了确立核心种源的竞争地位, 应重点加强本地优良种质资源的鉴评和利用。

关键词: 广东省, 栽培稻种, 遗传结构, 遗传演化, SLAF标签

Abstract:

Since the success of rice dwarfism breeding, Guangdong rice varieties have played an important role in domestic rice breeding. According to the national “14th Five-Year Plan”, the independent innovation of seed industry in China will aim at enhancing the competitiveness of core seed resources, and focus on the protection and utilization of germplasm resources. In this study, we carried out the analysis of genetic evolution, population genetic structure, and principal component analysis for 98 representative varieties including bred varieties in different periods and local varieties in Guangdong Province, and found that 43 old rice varieties and 5 local rice varieties had broader genetic basis, while 50 newly bred varieties had a relatively narrow genetic basis. Genetic evolution and pedigree analysis indicated that most of the old varieties originated from Guangchang 13, Nantehao, Aizizhan, Tangpuai and Zhuyin 2, while most of the new rice varieties were mainly derived from IR varieties, Jingxian 677, Guangchangai and Zhongxian 3588. These results indicated that the usage of foreign varieties had been strengthened in rice breeding and the utilization of the elite local germplasms was weakened, which may be related to the rising of three-line hybrid rice since 1980s. In conclusion, to establish the competitive position of core seed sources, the evaluation and utilization of local elite germplasms should be emphasized.

Key words: Guangdong province, cultivated rice resources, genetic structure, evolutionary relationship, SLAF tag

附表1

材料清单"

样号编号
No.
材料名称
Name of rice materials
选育单位
Breeding agencies
选育时期
Breeding period
R1
本院青小金早
Benyuanqingxiaojinzao
广东博罗县小金农场
Xiaojin farm of Boluo county, Guangdong Province
1960年
Breeded in 1960
R2
三七早
Sanqizao
惠阳地区农业科学研究所
Huiyang Institute of Agricultural Sciences
20世纪60-70年代
1960s-70s
R3
广场矮6号
Guangchang’ai 6
广东省农业科学研究院
Guangdong Academy of Agricultural Sciences
1959年
Breeded in 1959
R4
广陆矮4号
Guanglu’ai 4
广东省农业科学研究院
Guangdong Academy of Agricultural Sciences
1983、1984年审定
Approved in 1983 and 1984
R5
贵州余农2号
Guizhouyunong 2
贵州
Guizhou province
20世纪70年代
Breede in 1970s
R6
梅柳10号
Meiliu 10
广西柳州地区农业科学研究所
Liuzhou Institute of Agricultural Sciences Research
1972年
Breeded in 1972
R7
珍迁糯
Zhenqiannuo
广东肇庆农业科学研究所
Zhaoqing Institute of Agricultural Sciences
1969年选育
Breeded in 1969
R8
红梅早
Hongmeizao
新会环城农科站
Huancheng Station of Agricultural Sciences of Xinhui District
1985年审定
Breeded in 1985
R9
叶青伦
Yeqinglun
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1982年育成
Breeded in 1982
R10
青桂矮5号
Qinggui’ai 5
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪80年代
Breeded in 1980s
R11
三黄占2号
Sanhuangzhan 2
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪80年代
Breeded in 1980s
R12
双矮11
Shuang’ai 11
华南农业大学
South China Agricultural University
20世纪60年代
Breeded in 1960s
R13
红辐(早)2
Hongfuzao 2
广东省始兴县农业科学研究所
Shixing Instritute of Agricultural Sciences
20世纪60-70年代
Breeded in 1960s and 1970s
R14
科矮早9号
Ke’aizao 9
广东潮安县农业科学研究所
Chao’an Instritute of Agricultural Sciences
20世纪60-70年代
Breeded in 1960s and 1970s
R15
香丝苗2号
Xiangsimiao 2
广东省增城市农业科学研究所
Zhencheng Institute of Agricultural Sciences Research
1994年审定
Approved in 1994
R16
南丛3
Nancong 3
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪80年代
Breeded in 1980s
R17
桂野占2号
Guiyezhan 2
增城市种子站
Zengcheng Seed Station
20世纪80年代
Breeded in 1980s
R18
七青占
Qiqingzhan
广东省遂溪县良种场
Good Seed Farm in Suixi County
20世纪70-80年代
Breeded in 1970s-1980s
R19
新青92
Xinqing 92
广东省信宜县农业科学研究所
Xingyi Institution of Agricultural Sciences
20世纪70年代
Breeded in 1970s
R20
广科36
Guangke 36
广东省佛山市农业科学研究所
Foshan Institution of Agricultural Sciences Research
1986、1987审定
Approved in 1986 and 1987
R21
科麦糯
Kemainuo
惠来农业科学研究所
Huilai Institution of Agricultural Sciences
20世纪70、80年代
Breeded in 1970s-1980s
R22
汕优836-1
Shanyou 836-1
广东省连山县农业科学研究所
Lianshan Institution of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R23
青珍1号
Qingzhen 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R24
晚丰早1
Wanfengzao 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R25
南双矮
Nanshuang’ai
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R26
特三五1
Tesanwu 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R27
玉粳占2
Yugengzhan 2
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R28
芦香占3
Luxiangzhan 3
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R29
华丝占
Huasizhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R30
莉粳红米
Ligenghongmi
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R31
双粳占
Shuanggengzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R32
特籼占13
Teshanzhan 13
广东省佛山市农业科学研究所
Foshan Institution of Agricultural Sciences Research
1996年审定
Approved in 1996
R33
锦山占
Jingshanzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R34
矮珍占
Aizhenzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R35
丰八占
Fengbazhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2001年通过审定
Approved in 2001
R36
矮秀占
Yuexiuzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2000、2001年参加省区试
Participated in Provincial test in 2000 and 2001
R37
银花占
Yinhuazhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2005年审定
Approved in 2005
R38
中二软占
Zhong’erruanzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1999、2000年参加省区试
Participated in Provincial test in 1999 and 2000
R39
籼小占
Shanxiaozhan
佛山市农业科学研究所
Foshan Institute of Agricultural Sciences Research
1993、1994年审定
Approved in 1993 and 1994
R40
桂农占
Guinongzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2005年审定
Approved in 2005
R41
粤香占
Yuexiangzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1995年
Breeded in 1995
R42
绿黄占
Lvhuangzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1996年
Breeded in 1996
R43
巴三占
Basanzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1992年
Breeded in 1992
R44
二齐占
Erqizhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1992年
Breeded in 1992
R45
汉二糯
Han’ernuo
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1992年
Breeded in 1992
R46
北珍矮8号
Beizhen’ai 8
韶关地区农业科学研究所
Shaoguan Institute of Agricultural Sciences
1965-69年
Breeding from 1965 to 1969
R47
闷加黑丝
Menjiaheisi
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪70、80年代
Breeded in 1970s-1980s
R48
穗粳占
Suigengzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1997年
Breeded in 1997
R49
方源1
Fangyuan 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1997年
Breeded in 1997
R50
绿粳占1
Lvgengzhan 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1995年
Breeded in 1995
R51
源珍397
Yuanzhen 397
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1995年
Breeded in 1995
R52
七澳占1
Qi’aozhan 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1995年
Breeded in 1995
R53
青华矮6
Qinghua’ai 6
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1984年审定
Approved in 1984
R54
迁杂1
Qianza 1
华南农业大学
South China Agricultral University
20世纪70年代
Breeded in 1970s
R55
矮黑糯
Aiheinuo
肇庆地区农业科学研究所
Zhaoqing Institute of Agricultural Sciences
1982年审定
Approved in 1982
R56
新包矮
Xinbao’ai
高要县农业科学研究所
Gaoyao Institute of Agricultural Sciences
20世纪80年代
Breeded in 1980s
R57
惠优占
Huiyouzhan
广东省惠阳地区农业科学研究所
Huiyang Institute of Agricultural Sciences Research
1981、1982年省区试
Participated in Provincial test in 1981 and 1982
R58
广恢312
Guanghui 312
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
20世纪90年代
Breeded in 1990s
R59
新铁大
Xintieda
潮安农业科学研究所
Chao’an Institute of Agricultural Sciences
1978年审定
Approved in 1978
R60
胜泰1号
Shengtai 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1999年审定
Approved in 1999
R61
粳籼89
Gengxian 89
广东省佛山市农业科学研究所
Foshan Institution of Agricultural Sciences Research
1990、1991年省区试
Participated in Provincial test in 1990 and 1991
R62
广场13
Guangchang 13
广东华南农业科学研究所
South China Institute of Agricultural Sciences
1953年
Breeded in 1953
R63
矮脚南特
Aijiaonante
广东潮阳县
Chaoyang county, Guangdong province
1956年
Breeded in 1956
R64
广秋矮
Guangqiu’ai
广东省农业科学研究院
Guangdong Academy of Agricultural Sciences
1963年
Breeded in 1963
R65
饶平矮
Raoping’ai
广东省饶平县农业科学研究所
Raoping Institute of Agricultural Sciences
1964年
Breeded in 1964
R66
早金凤5号
Zaojinfeng 5
广东省沙田县农业科学研究所
Shatian Institute of Agricultural Sciences
1964年
Breeded in 1964
R67
双竹占
Shuangzhuzhan
广东省农业科学研究院
Guangdong Academy of Agricultural Sciences
1966年
Breeded in 1966
R68
桂朝2号
Guichao 2
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1976年
Breeded in 1976
R69
双桂1号
Shuanggui 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1979年
Breeded in 1979
R70
三二矮
San’er’ai
广东省龙门县农业科学研究所
Longmen Institute of Agricultural Sciences
1983年
Breeded in 1983
R71
双桂36
Shuanggui 36
广东省农业科学院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1979年
Breeded in 1979
R72
七桂早25
Qiguizao 25
广东省佛山市农业科学研究所
Foshan Institution of Agricultural Sciences Research
1985年
Breeded in 1985
R74
特青2号
Teqing 2
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1986、1987年参加省区试
Participated in Provincial test in 1986 and 1987
R75
青六矮1号
Qingliu’ai 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1988、1989年参加区试
Participated in Provincial test in 1988 and 1989
R76
七山占
Qishanzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1989年参加省区试
Participated in Provincial test in 1989
R77
粤航1号
Yuehang 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2005年审定
Approved in 2005
R78
美香占
Meixiangzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2006年审定
Approved in 2006
R79
软红米
Ruanhongmi
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2006年
Breeded in 2006
R80
航香糯
Hangxiangnuo
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2009年
Breeded in 2009
R81
粤晶丝苗2号
Yuejingsimiao 2
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2006年
Breeded in 2006
R82
窄叶青8号
Zhaiyeqing 8
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1971年
Breeded in 1971
R83
三五糯1号
Sanwunuo 1
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
1987年育成
Breeded in 1987
R84
粤农占
Yuenongzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2003年审定
Approved in 2003
R85
黄华占
Huanghuazhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2005年审定
Approved in 2005
R86
玉香油占
Yuxiangyouzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2003、2004年参加省区试
Participated in Provincial test in 2003 and 2004
R87
粤丰占
Yuefengzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2003年国审
National Approval in 2003
R88
丰华占
Fenghuazhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2003年国审
National Approval in 2003
R90
粤农丝苗
Yuenongsimiao
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2011年审定
Approved in 2011
R91
五山丝苗
Wushansimiao
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2009年审定
Approved in 2009
R92
银晶软占
Yinjingruanzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2003、2004年参加省区试
Participated in Provincial test in 2003 and 2004
R93
合丰占
Hefengzhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2009年审定
Approved in 2009
R94
金农丝苗
Jinnongsimiao
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2010年审定
Approved in 2010
R95
丰美占
Fengmeizhan
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2006年国审
National Approval in 2006
R96
齐粒丝苗
Qilisimiao
广东省农业科学研究院水稻研究所
Rice Research Institute, Guangdong Academy of Agricultural Sciences
2004年审定
Approved in 2004
R97
鼠牙占
Shuyazhan
广东
Guangdong province
R98
金包银
Jinbaoyin
广东
Guangdong province
R99
龙牙占
Longyazhan
广东
Guangdong province
R100
白壳丝苗
Baikesimiao
广东省农业科学研究院
Guangdong Academy of Agricultural Sciences
1930年
Breeded in 1930
R101
油占
Youzhan
广东
Guangdong province
R102
早油占
Zaoyouzhan
广东
Guangdong province

图1

SLAF标签(A)和SNP (B)在染色体上的分布"

附表2

各样品测序数据统计表"

样品编号
Sample ID
Reads数量
Total Reads
Q30
Percentage (%)
GC含量
Percentage (%)
样品编号
Sample ID
Reads数量
Total Reads
Q30
Percentage (%)
GC含量
Percentage (%)
R1 635,920 86.42 46.03 R52 531,911 85.75 45.91
R2 578,940 87.31 45.58 R53 369,113 86.26 47.82
R3 500,692 84.86 47.85 R54 529,914 86.39 46.85
R4 664,094 86.02 46.65 R55 396,752 86.4 49.29
R5 532,257 84.52 45.91 R56 486,065 85.26 47.15
R6 345,441 87.11 46.37 R57 569,603 86.77 46.31
R7 337,445 87.39 45.96 R58 392,047 86.53 46.21
R8 438,132 87.43 45.94 R59 480,892 86.83 45.84
R9 540,697 85.05 46.14 R60 525,921 86.39 46.31
R10 494,598 85 45.93 R61 409,236 84.8 47.9
R11 643,295 85.24 46.21 R62 460,737 86.47 46.68
R12 562,185 85.23 46.47 R63 294,675 83.85 50.22
R13 303,915 87.09 46.5 R64 576,566 85.9 46.45
R14 321,807 86.84 46.08 R65 486,090 85.35 46.74
R15 476,794 85.6 45.87 R66 339,593 86.3 47.1
R16 513,699 84.54 46.27 R67 446,435 86.65 46.75
R17 405,962 86 45.8 R68 454,768 85.14 49.21
R18 477,976 84.74 46.62 R69 351,216 85.86 49.1
R19 622,205 86.84 46.22 R70 428,678 86.95 46.39
R20 271,777 86.67 46.24 R71 423,922 85.9 47.6
R21 499,466 85.97 46.91 R72 261,140 85.92 47.85
R22 478,179 86.44 46.58 R74 294,894 85.72 49.44
R23 518,491 86.22 46.09 R75 326,833 85.71 48.04
R24 342,310 87.1 46.52 R76 262,823 83.67 49.38
R25 583,246 85.61 46.36 R77 453,164 81.73 47.01
R26 331,701 87.55 45.86 R78 463,065 87.11 45.8
R27 375,733 87.65 46.03 R79 536,647 86.52 46.08
R28 413,405 87.5 46.66 R80 515,222 86.42 45.65
R29 595,884 86.68 46.08 R81 498,109 85.29 45.5
R30 512,709 87.54 45.27 R82 326,794 84.23 49.16
R31 550,233 86.57 46.43 R83 390,651 84.35 47.94
R32 369,778 86.57 46.69 R84 303,474 83.58 48.87
R33 304,867 86.57 46.75 R85 686,652 84.7 44.74
R34 337,392 86.19 46.43 R86 387,754 87.39 46.52
R35 491,432 86.34 46.1 R87 319,066 84.04 49
R36 439,535 86.39 45.45 R88 346,813 84.44 48.03
R37 356,037 86.87 46.21 R90 270,170 83.35 49.13
R38 311,488 83.98 46.26 R91 586,309 86.5 45.62
R39 542,467 86.39 45.94 R92 500,155 86.38 45.91
R40 361,218 86.33 46.45 R93 319,622 85.31 48.46
R41 738,154 87.28 45.6 R94 644,233 87.02 45.76
R42 341,669 87.26 46.19 R95 452,928 85.79 46.46
R43 589,762 86.02 46.06 R96 518,862 86.89 45.81
R44 424,456 85.82 46.12 R97 569,385 86.81 46.54
R45 442,996 86.03 47.76 R98 234,438 81.85 53.98
R46 372,099 86.05 46.34 R99 423,804 84.53 47.26
R47 247,736 86.64 46.27 R100 263,923 82.56 51.86
R48 464,998 86.26 46.03 R101 398,233 85.09 46.61
R49 579,832 86.28 46.15 R102 383,906 84.57 47.76
R50 420,698 87.71 45.74 Arab 209,385 86.77 42.96
R51 488,794 87 46.08

附表3

各样品SLAF标签数统计"

样品编号
Sample ID
样品所含SLAF标签数
SLAF number
测序总深度
Total depth
平均深度
Average depth
样品编号
Sample ID
样品所含SLAF标签数
SLAF number
测序总深度
Total depth
平均深度
Average depth
R1 15,071 257,705 17.1 R51 15,062 211,441 14.04
R2 14,920 265,447 17.79 R52 14,707 232,638 15.82
R3 14,877 179,042 12.03 R53 14,462 135,518 9.37
R4 14,956 262,167 17.53 R54 15,114 218,166 14.43
R5 15,657 198,184 12.66 R55 13,462 110,209 8.19
R6 14,550 150,644 10.35 R56 15,194 200,693 13.21
R7 14,011 135,024 9.64 R57 15,496 256,324 16.54
R8 14,848 176,348 11.88 R58 14,713 168,457 11.45
R9 14,715 239,714 16.29 R59 15,032 211,747 14.09
R10 14,951 213,623 14.29 R60 15,096 226,648 15.01
R11 14,757 274,846 18.62 R61 14,529 137,455 9.46
R12 15,070 226,872 15.05 R62 14,993 193,631 12.91
R13 14,068 120,655 8.58 R63 13,399 73,731 5.5
R14 14,281 130,210 9.12 R64 14,692 217,789 14.82
R15 14,829 201,179 13.57 R65 15,355 191,853 12.49
R16 14,904 214,861 14.42 R66 14,194 124,705 8.79
R17 14,794 182,221 12.32 R67 16,100 190,851 11.85
R18 14,766 206,509 13.99 R68 14,391 117,228 8.15
R19 15,209 265,128 17.43 R69 14,286 111,057 7.77
R20 14,258 120,387 8.44 R70 14,882 175,186 11.77
R21 14,181 191,486 13.5 R71 14,681 149,065 10.15
R22 14,793 208,879 14.12 R72 13,636 89,413 6.56
R23 14,980 229,325 15.31 R74 13,722 79,851 5.82
R24 14,351 142,647 9.94 R75 14,278 112,349 7.87
R25 15,002 226,103 15.07 R76 13,793 82,927 6.01
R26 13,680 140,677 10.28 R77 14,621 126,317 8.64
R27 15,221 163,316 10.73 R78 14,555 186,233 12.8
R28 14,655 158,257 10.8 R79 15,498 235,175 15.17
R29 15,100 263,791 17.47 R80 14,307 207,041 14.47
R30 14,584 192,716 13.21 R81 14,845 222,057 14.96
R31 15,164 252,288 16.64 R82 14,683 107,365 7.31
R32 14,521 161,758 11.14 R83 15,521 134,295 8.65
R33 14,379 127,040 8.84 R84 14,185 98,126 6.92
R34 14,421 145,774 10.11 R85 14,964 256,396 17.13
R35 14,759 220,263 14.92 R86 14,648 167,549 11.44
R36 14,701 168,149 11.44 R87 14,668 113,095 7.71
R37 14,616 147,532 10.09 R88 14,635 131,765 9
R38 14,187 130,106 9.17 R90 13,951 85,067 6.1
R39 15,466 248,844 16.09 R91 14,820 256,649 17.32
R40 14,668 155,078 10.57 R92 14,924 221,591 14.85
R41 15,165 324,856 21.42 R93 14,409 109,255 7.58
R42 14,291 147,775 10.34 R94 15,103 291,762 19.32
R43 14,815 257,871 17.41 R95 14,663 174,257 11.88
R44 14,575 180,868 12.41 R96 14,942 239,334 16.02
R45 13,918 129,268 9.29 R97 16,106 231,349 14.36
R46 14,546 158,715 10.91 R98 10,162 39,227 3.86
R47 14,245 106,700 7.49 R99 14,596 159,372 10.92
R48 14,861 209,942 14.13 R100 11,941 45,001 3.77
R49 14,895 253,194 17 R101 14,625 145,866 9.97
R50 14,683 159,316 10.85 R102 14,641 144,285 9.85

表1

SLAF标签和多态性 SLAF标签染色体分布统计"

染色体编号
Chr. ID
SLAF标签数
SLAF number
多态性SLAF标签数
Polymorphic SLAF
Chr.1 2098 1074
Chr.2 1149 729
Chr.3 1358 1006
Chr.4 1295 815
Chr.5 1757 888
Chr.6 1987 1,048
Chr.7 1823 1,014
Chr.8 1679 888
Chr.9 1500 832
Chr.10 1461 897
Chr.11 1423 805
Chr.12 1105 571
Chr.Un 16 7
Chr.Sy 44 36
总计Total 18,695 10,610

附表4

样品SNP信息统计"

样品编号
Sample ID
检测到的SNP总数
Total SNP
样品的SNP数
SNP num
SNP完整度
Integrity
SNP杂合率
Heter ratio
R1 43,430 15,753 36.27% 36.80%
R2 43,430 15,192 34.98% 34.35%
R3 43,430 15,050 34.65% 32.75%
R4 43,430 15,233 35.07% 35.15%
R5 43,430 16,940 39.01% 46.95%
R6 43,430 14,727 33.91% 31.25%
R7 43,430 14,000 32.24% 32.55%
R8 43,430 14,884 34.27% 32.79%
R9 43,430 15,008 34.56% 33.36%
R10 43,430 14,824 34.13% 33.43%
R11 43,430 15,885 36.58% 35.62%
R12 43,430 15,674 36.09% 36.00%
R13 43,430 13,273 30.56% 29.32%
R14 43,430 14,198 32.69% 30.98%
R15 43,430 14,797 34.07% 33.55%
R16 43,430 15,350 35.34% 34.10%
R17 43,430 14,436 33.24% 34.50%
R18 43,430 14,441 33.25% 32.19%
R19 43,430 15,889 36.59% 37.26%
R20 43,430 13,255 30.52% 27.82%
R21 43,430 13,047 30.04% 30.87%
R22 43,430 14,992 34.52% 32.77%
R23 43,430 15,186 34.97% 34.47%
R24 43,430 14,839 34.17% 33.07%
R25 43,430 15,978 36.79% 35.25%
R26 43,430 12,253 28.21% 26.77%
R27 43,430 16,492 37.97% 47.22%
R28 43,430 14,328 32.99% 33.19%
R29 43,430 16,141 37.17% 37.38%
R30 43,430 14,402 33.16% 32.59%
R31 43,430 15,586 35.89% 35.19%
R32 43,430 14,961 34.45% 35.00%
R33 43,430 14,141 32.56% 31.62%
R34 43,430 14,898 34.30% 32.74%
R35 43,430 15,174 34.94% 32.89%
R36 43,430 14,016 32.27% 31.71%
R37 43,430 14,186 32.66% 32.67%
R38 43,430 14,210 32.72% 30.87%
R39 43,430 17,061 39.28% 41.26%
R40 43,430 14,981 34.49% 31.01%
R41 43,430 16,996 39.13% 40.10%
R42 43,430 14,691 33.83% 31.08%
R43 43,430 15,463 35.60% 35.17%
R44 43,430 13,706 31.56% 30.48%
R45 43,430 13,347 30.73% 28.98%
R46 43,430 14,922 34.36% 33.27%
R47 43,430 10,721 24.69% 29.03%
R48 43,430 15,259 35.13% 33.65%
R49 43,430 14,288 32.90% 36.10%
R50 43,430 15,437 35.54% 30.45%
R51 43,430 15,760 36.29% 35.74%
R52 43,430 14,970 34.47% 33.53%
R53 43,430 13,970 32.17% 29.76%
R54 43,430 15,550 35.80% 37.05%
R55 43,430 10,929 25.16% 27.60%
R56 43,430 15,476 35.63% 42.91%
R57 43,430 17,426 40.12% 44.63%
R58 43,430 14,029 32.30% 32.35%
R59 43,430 15,361 35.37% 33.64%
R60 43,430 15,184 34.96% 33.94%
R61 43,430 13,798 31.77% 29.58%
R62 43,430 15,259 35.13% 34.24%
R63 43,430 10,777 24.81% 23.01%
R64 43,430 14,968 34.46% 34.55%
R65 43,430 16,127 37.13% 39.83%
R66 43,430 13,150 30.28% 28.43%
R67 43,430 18,006 41.46% 51.47%
R68 43,430 13,435 30.93% 28.26%
R69 43,430 13,178 30.34% 25.85%
R70 43,430 15,854 36.50% 35.08%
R71 43,430 14,404 33.17% 32.17%
R72 43,430 12,466 28.70% 25.12%
R74 43,430 12,254 28.22% 26.64%
R75 43,430 13,093 30.15% 27.48%
R76 43,430 12,058 27.76% 23.10%
R77 43,430 13,557 31.22% 29.45%
R78 43,430 14,624 33.67% 31.13%
R79 43,430 16,729 38.52% 46.27%
R80 43,430 14,142 32.56% 31.04%
R81 43,430 15,395 35.45% 32.90%
R82 43,430 13,506 31.10% 31.82%
R83 43,430 15,469 35.62% 44.26%
R84 43,430 12,287 28.29% 25.84%
R85 43,430 16,305 37.54% 36.11%
R86 43,430 15,180 34.95% 32.83%
R87 43,430 13,957 32.14% 31.58%
R88 43,430 14,000 32.24% 28.78%
R90 43,430 11,753 27.06% 25.70%
R91 43,430 16,048 36.95% 35.60%
R92 43,430 15,131 34.84% 32.89%
R93 43,430 13,055 30.06% 28.44%
R94 43,430 16,343 37.63% 37.25%
R95 43,430 16,289 37.51% 34.31%
R96 43,430 15,473 35.63% 33.81%
R97 43,430 18,190 41.88% 53.41%
R98 43,430 8,193 18.86% 20.83%
R99 43,430 13,992 32.22% 31.85%
R100 43,430 9,641 22.20% 24.90%
R101 43,430 14,044 32.34% 30.37%
R102 43,430 13,356 30.75% 27.51%

图2

100份栽培稻的进化树 红色代表广东省于20世纪50-80年代育成的老品种; 蓝色代表广东省于20世纪90年代及以后育成的新品; 绿色代表地方稻; 紫色代表广东省外品种。"

附图1

第一类群中材料系谱图 红框代表本文中的栽培稻,蓝框代表共有的血缘亲本."

附图2

第二类群中材料系谱图 红框代表本文中的栽培稻,蓝框代表共有的血缘亲本."

图3

100份栽培稻分群数(K-value)为1~10的聚类图 图A中每种颜色代表一个群, 每行代表一个分群值的情况; 图B为每个K值对应的ΔK值。图B中小红圈表示当K = 3时, CV最小, 因此3为推荐分群数。"

附图3

第三类群第一亚类中材料系谱图 红框代表本文中的栽培稻,蓝框代表共有的血缘亲本."

附图4

第三类群第二亚类第1小类材料系谱图 红框代表本文中的栽培稻,蓝框代表共有的血缘亲本."

附图5

第三类群第二亚类第2小类材料系谱图 红框代表本文中的栽培稻,蓝框代表共有的血缘亲本."

表2

水稻材料在群体结构分类与进化树分类中的对比"

材料编号
Material number
群体结构分类
Structure number
进化树分类
Cluster
number
材料类型
Type of
materials
材料编号
Material
number
群体结构分类
Structure number
进化树分类
Cluster
number
材料类型
Type of
materials
R81 A Cluster III Sub-group 2 GD-N R67 A Cluster I GD-O
R35 A Cluster III Sub-group 2 GD-N R47 A Cluster II GD-O
R32 A Cluster III Sub-group 2 GD-N R75 A Cluster III Sub-group 2 GD-O
R78 A Cluster III Sub-group 2 GD-N R23 A Cluster III Sub-group 2 GD-N
R93 A Cluster III Sub-group 2 GD-N R41 A Cluster III Sub-group 2 GD-N
R96 A Cluster III Sub-group 2 GD-N R82 A Cluster I GD-O
R94 A Cluster III Sub-group 2 GD-N R18 A Cluster III Sub-group 1 GD-O
R27 A Cluster III Sub-group 2 GD-N R98 A Cluster I GD-L
R90 A Cluster III Sub-group 2 GD-N R53 A Cluster I GD-O
R20 A Cluster III Sub-group 2 GD-O R64 B Cluster I GD-O
R22 A Cluster III Sub-group 2 GD-N R56 B Cluster I GD-O
R33 A Cluster III Sub-group 2 GD-N R45 B Cluster III Sub-group 2 GD-N
R31 A Cluster III Sub-group 2 GD-N R100 B Cluster I GD-O
R92 A Cluster III Sub-group 2 GD-N R55 B Cluster I GD-O
R61 A Cluster III Sub-group 2 GD-N R54 B Cluster I GD-O
R49 A Cluster III Sub-group 2 GD-N R9 B Cluster II GD-O
材料编号
Material number
群体结构分类
Structure number
进化树分类
Cluster
number
材料类型
Type of
materials
材料编号
Material
number
群体结构分类
Structure number
进化树分类
Cluster
number
材料类型
Type of
materials
R84 A Cluster III Sub-group 2 GD-N R21 B Cluster II GD-O
R60 A Cluster III Sub-group 2 GD-N R65 B Cluster II GD-O
R39 A Cluster III Sub-group 2 GD-N R101 B Cluster II GD-L
R38 A Cluster III Sub-group 2 GD-N R97 B Cluster II GD-L
R86 A Cluster III Sub-group 2 GD-N R5 B Cluster II OPV
R88 A Cluster III Sub-group 2 GD-N R14 B Cluster II GD-O
R36 A Cluster III Sub-group 2 GD-N R13 B Cluster II GD-O
R91 A Cluster III Sub-group 2 GD-N R102 B Cluster II GD-L
R37 A Cluster III Sub-group 2 GD-N R63 B Cluster II GD-O
R85 A Cluster III Sub-group 2 GD-N R99 B Cluster II GD-L
R50 A Cluster III Sub-group 2 GD-N R66 B Cluster II GD-O
R58 A Cluster III Sub-group 2 GD-N R1 B Cluster II GD-O
R79 A Cluster III Sub-group 2 GD-N R4 B Cluster II GD-O
R48 A Cluster III Sub-group 2 GD-N R2 B Cluster II GD-O
R34 A Cluster III Sub-group 2 GD-N R3 B Cluster II GD-O
R57 A Cluster III Sub-group 2 GD-O R7 B Cluster II GD-O
R28 A Cluster III Sub-group 2 GD-N R62 B Cluster II GD-O
R11 A Cluster III Sub-group 2 GD-O R6 B Cluster II OPV
R87 A Cluster III Sub-group 2 GD-N R8 B Cluster II GD-O
R43 A Cluster III Sub-group 2 GD-N R46 B Cluster II GD-O
R29 A Cluster III Sub-group 2 GD-N R71 C Cluster III Sub-group 2 GD-O
R15 A Cluster III Sub-group 2 GD-N R16 C Cluster III Sub-group 2 GD-O
R42 A Cluster III Sub-group 2 GD-N R12 C Cluster III Sub-group 2 GD-O
R44 A Cluster III Sub-group 2 GD-N R68 C Cluster III Sub-group 2 GD-O
R80 A Cluster III Sub-group 2 GD-N R69 C Cluster III Sub-group 2 GD-O
R77 A Cluster III Sub-group 2 GD-N R59 C Cluster III Sub-group 2 GD-O
R40 A Cluster III Sub-group 2 GD-N R25 C Cluster III Sub-group 2 GD-N
R30 A Cluster III Sub-group 2 GD-N R74 C Cluster III Sub-group 2 GD-O
R26 A Cluster III Sub-group 2 GD-N R70 C Cluster III Sub-group 2 GD-O
R76 A Cluster III Sub-group 1 GD-O R24 C Cluster III Sub-group 2 GD-N
R51 A Cluster III Sub-group 2 GD-N R19 C Cluster III Sub-group 2 GD-O
R83 A Cluster III Sub-group 1 GD-O R10 C Cluster III Sub-group 2 GD-O
R95 A Cluster III Sub-group 2 GD-N R52 C Cluster III Sub-group 2 GD-N
R72 A Cluster III Sub-group 1 GD-O R17 C Cluster III Sub-group 2 GD-O

图4

100份栽培稻的PCA聚类图 I: 红色圆点代表广东20世纪80年代(包括80年代)以前育成的老品种; II: 蓝色圆点代表广东20世纪90年代以后育成的新品种; III: 绿色圆点代表地方稻种; IV: 紫色圆点代表广东省外品种。"

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