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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (4): 568-577.doi: 10.3724/SP.J.1006.2019.83052

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Excavation of main candidate genome regions in Suwan germplasm improvement process of maize

LI Xiu-Shi,WU Xun,WU Wen-Qiang,LIU Peng-Fei,GUO Xiang-Yang,WANG An-Gui,ZHU Yun-Fang,CHEN Ze-Hui()   

  1. Upland Crops Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
  • Received:2018-06-26 Accepted:2018-12-24 Online:2019-04-12 Published:2019-01-04
  • Contact: Ze-Hui CHEN E-mail:chenzh907@sina.com
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2016YFD0101206);Innovation Program of QAAS(Special Character of Independent Innovation of Guizhou Academy of Agriculture [2014]006);National Natural Science Foundation of China(31760387);Science and Technology Support Project of Guizhou Province (Qiankehe support([2016]2605, [2016]2549, [2017]2507, [2018]2296);Science and Technology Project of Guizhou Province (Qiankehe Foundation)([2017]1413)

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Abstract:

Suwan germplasm with good resistance, strong adaptability and excellent grain quality has played an irreplaceable role in modern breeding, especially in the southern of China. It is important to clarify the genetic mechanism of Suwan germplasm. In this study, modified generations of Suwan 1 (Suwan 1 C10) and its derived population (Suwan-Lancaster 1 C0) were used to be genotyped by using MaizeSNP50 chips containing about 56,000 SNP markers. There was a smaller genome differences among different improved generations for Suwan 1 population, with only five different inherited fragments identified, among which four appeared only in the 11th improved generation (Suwan 1 C11), one appeared only in the 15th improved generation (Suwan 1 C15). For Suwan-Lancaster1 population, among 18 different genetic fragments eight were stably inherited in different improved generations. A total of 43 specific genetic segments of Lancaster germplasm were obtained, among them 35 were stably inherited in different improved generations. Genome-wide association studies (GWAS) showed that 16 QTNs significantly associated with kernel row number were located on chromosomes 2, 3, 5, 6, 7, 8, and 9, respectively, among them SYN25713 and SYN36577 were located in the Lancaster specific genetic fragment of the Suwan-Lancaster 1 population. A total of 13 QTNs related to ear length were located on chromosomes 1, 2, 5, 7, 8, and 9, respectively, among them PZE-105143697 was located in the Lancaster specific genetic fragment. These results provide an important theoretical basis for the subsequent genome-wide association study and molecular marker assisted selection.

Key words: maize, population improvement, genome characteristics, genome-wide association study, genetic loci

Table 1

Pedigree and groups of accessions used in this paper"

序号
No.		 材料
Accession		 系谱
Pedigree		 类群
Group
1 Suwan 1 (Suwan 1 C10) Suwan 1 C9 Suwan
2 Suwan 1 C11 Suwan 1 C10 Suwan
3 Suwan 1 C12 Suwan 1 C11 Suwan
4 Suwan 1 C13 Suwan 1 C12 Suwan
5 Suwan 1 C15 Suwan 1 C14 Suwan
6 苏兰1号C0 SL1C0 Suwan, Lancaster及78599选系
Synthetic populations of Suwan, Lancaster and 78599 selected lines		 Suwan-Lancaster
7 苏兰1号C1 SL1C1 苏兰1号C0 SL1C0 Suwan-Lancaster
8 苏兰1号C2 SL1C2 苏兰1号C1 SL1C1 Suwan-Lancaster
9 苏兰1号C3 SL1C3 苏兰1号C2 SL1C2 Suwan-Lancaster

Table 2

Ear length and ear row number of nine tested groups"

材料
Accession		 穗长 Ear length 穗行数 Kernel row number
贵阳
Guiyang		 大方
Dafang		 罗平
Luoping		 平均值
Mean		 贵阳
Guiyang		 大方
Dafang		 罗平
Luoping		 平均值
Mean
苏兰1号C0 SL1C0 17.67 18.77 17.40 17.94 15.47 14.53 14.67 14.89
苏兰1号C1 SL1C1 18.13 19.33 17.17 18.21 15.33 14.73 14.27 14.78
苏兰1号C2 SL1C2 17.87 18.97 18.20 18.34 14.27 14.27 14.47 14.33
苏兰1号C3 SL1C3 18.27 19.57 17.73 18.52 15.00 15.53 15.20 15.24
Suwan 1 (Suwan 1 C10) 17.47 18.33 16.43 17.41 15.00 14.93 14.00 14.64
Suwan 1 C11 17.67 18.23 17.03 17.64 15.40 14.93 14.13 14.82
Suwan 1 C12 16.87 17.97 16.33 17.06 15.13 15.87 14.60 15.20
Suwan 1 C13 16.53 18.17 16.20 16.97 15.40 14.93 14.20 14.84
Suwan 1 C15 17.60 18.53 17.03 17.72 14.60 14.60 14.53 14.58
平均值Mean 17.56 18.65 17.06 17.76 15.07 14.93 14.45 14.81
标准差Standard deviation 1.09 0.73 0.84 1.11 0.67 0.57 0.65 0.68
变异系数Coefficient of variation (%) 6.21 3.91 4.92 6.25 4.45 3.82 4.50 4.59

Fig. 1

Genomic characteristics of Suwan 1 in different improved generations The physical location of the specific SNP markers on chromosome is shown in the Supplementary table 1."

Table 1

1 Supplementary table 1 Specific markers for different improvement generations of Suwan 1 population"

SNP 染色体
Chr.		 物理位置
Position		 SNP 染色体
Chr.		 物理位置
Position
SYN450 1 35968064 PZE-106016986 6 32497838
PZE-103104159 3 164159285 PZE-106016987 6 32498979
PZE-106016953 6 32495316 PZE-106017115 6 32905813
PZE-106016962 6 32495710 PZE-106017122 6 32908494
PZE-106016971 6 32496071 PZE-106099248 6 152896893
PZA00540.3 6 32496071 PZE-108113902 8 163858777

Fig. 2

Genomic characteristics of Suwan-Lancaster1 in different improved generations The physical location of the specific SNP markers on chromosome is shown in Supplementary table 2."

Table 2

2 Supplementary table 2 Specific markers for different improvement generations of Suwan-Lancaster 1 population"

SNP 染色体
Chr.		 物理位置
Position		 SNP 染色体
Chr.		 物理位置
Position
PZE-101205609 1 253344590 PZE-102156731 2 203902578
PZE-101205965 1 253895960 SYN15645 3 182660027
SYN6838 1 297376850 PZE-105016506 4 7204051
PZE-103008521 2 4666469 PZE-106033525 5 76988770
PZE-102060229 2 38551101 SYN25006 6 8192709
PZE-102060230 2 39031517 PZE-107126153 7 163083361
PZE-102061400 2 39748797 PZE-109019803 7 20222259
SYN26925 2 200353907 PZE-109051268 9 85880947
SYN26929 2 200359094 PZE-109051619 9 86414796
SYN10568 2 200723525 PZE-109052137 9 86974491
SYN35589 2 201246108

Fig. 3

Genomic characteristics between Suwan 1 and Suwan-Lancaster 1 in different improved generations The physical location of the specific SNP markers on chromosome is shown in Supplementary table 3."

Table 3

3 Supplementary table 3 Specific markers between Suwan 1 and Suwan-Lancaster 1 in different improved generations"

SNP 染色体
Chr.		 物理位置
Position		 SNP 染色体
Chr.		 物理位置
Position
SYN11491 1 3683507 PZE-104127854 4 212788677
PZE-101054452 1 38617583 PZE-104127855 4 212788991
PZE-101178005 1 222370910 PZE-104152999 4 243521349
PZE-101192090 1 237838603 SYN28825 5 7319620
PZE-101192133 1 237900682 PZE-105051178 5 43960922
PZE-101192647 1 238680213 PZE-105051179 5 43961044
PZE-101195574 1 242361972 PZE-105051200 5 43966297
PZE-101195592 1 242398910 PZE-105099516 5 146942464
PZE-101196147 1 243255282 PZE-105101687 5 152095801
PZE-101196704 1 244083020 PZE-105102557 5 154315332
PZE-101196940 1 244512792 PZE-105144984 5 197943057
PZE-101197050 1 244678601 PZB02424.1 5 199531408
SYN12881 1 245242156 SYN30468 5 199531778
PZE-101197856 1 245308899 PZA00540.3 6 32496071
SYN15061 1 261370341 PZE-106016971 6 32496071
PZE-102060229 2 38551101 PZE-106017115 6 32905813
PZE-102060230 2 39031517 PZE-106017122 6 32908494
SYN26925 2 200353907 SYN25006 7 8192709
SYN26929 2 200359094 PZE-107018281 7 15776884
SYN35589 2 201246108 PZE-107126153 7 163083361
PZE-103025362 3 17738644 SYN34213 8 5090046
PZE-103056619 3 68433447 PZE-108010963 8 11645850
PZE-103068285 3 108233400 PUT-163a-78089347-4225 8 169951365
PZE-103076844 3 123683053 PUT-163a-78089347-4224 8 169951478
PZE-103083872 3 135004208 PZE-109008703 9 9247324
SYN34685 4 202660380 SYN36362 9 9247324
PZE-104126691 4 210495187 PZE-109051619 9 86414796
PZE-104127248 4 211708774 PZE-109101971 9 141650742
PZE-104127853 4 212785374 PZE-110080467 10 134211006

Table 3

Association of SNP loci with kernel rows per ear"

SNP 染色体
Chr.		 物理位置
Position		 P值
P-value (×10-4)		 最小等位基因频率
Minimum allele frequency
PZE-102049428 2 27586143 0.83 0.22
SYN29936 3 214728752 0.79 0.53
SYN25713 4 218657640 0.50 0.39
PZE-104012465 4 10671690 0.95 0.39
PZE-105068275 5 70167652 0.38 0.50
SYN35408 5 64502995 0.64 0.53
ZM013904-0312 5 64757602 0.64 0.53
PZE-105060180 5 58448124 0.80 0.44
PZE-106105143 6 155807238 0.29 0.42
PUT-163a-60355888-2779 6 30864359 0.32 0.61
PUT-163a-60355888-2773 6 30864423 0.32 0.61
SYN36577 7 9216854 0.53 0.67
SYN36527 8 166695438 0.72 0.17
SYN36532 8 166695690 0.72 0.83
PZE-108065598 8 115805296 0.89 0.33
PZE-109004718 9 5289730 0.54 0.31

Fig. 4

Kernel rows per ear related QTN"

Table 4

Association of SNP loci with ear length"

SNP 染色体
Chr.		 物理位置
Position		 P值
P-value (×10-4)		 最小等位基因频率
Minimum allele frequency
SYN28790 1 198085193 3.55 0.56
PZE-102089207 2 89322082 3.55 0.83
PZE-102089216 2 89350485 7.42 0.17
PZE-102094273 2 103594813 7.42 0.28
PZE-103146876 3 199472604 5.85 0.64
PZE-105143697 5 196993540 6.06 0.22
SYN2938 5 212502760 2.47 0.44
PZE-105181391 5 215066204 8.77 0.22
SYN19052 7 125475003 6.64 0.78
SYN10053 8 1816317 7.98 0.39
PZA-000908002 8 99959553 2.84 0.44
PZE-108076469 8 130589109 3.55 0.83
PZE-109008801 9 9401106 7.42 0.44

Fig. 5

Ear length related QTN"

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