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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (10): 2475-2482.doi: 10.3724/SP.J.1006.2022.14187

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

Construction of SNP high-density genetic map and QTL analysis of agronomic traits in cowpea (Vigna unguiculata (L.) Walp.)

LI Jian-Ling1,2(), GONG Dan2,3, WANG Su-Hua2, CHEN Hong-Lin2, CHENG Xu-Zhen2, XIONG Tao1,*(), WANG Li-Xia2,*()   

  1. 1College of Life Science, Yangtze University, Jingzhou 434025, Hubei, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3School of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
  • Received:2021-10-15 Accepted:2022-01-05 Online:2022-10-12 Published:2022-02-23
  • Contact: XIONG Tao,WANG Li-Xia E-mail:1411420008@qq.com;xiongtao@hotmail.com;wanglixia03@caas.cn
  • Supported by:
    National Key Research and Development Program of China(2019YFD1001300);National Key Research and Development Program of China(2019YFD1001303);China Agriculture Research System of MOF and MARA (Food Legume, CARS-08)

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Abstract:

To promote efficient utilization of cowpea germplasm resources and new gene discovery, a genetic linkage map containing 2984 Bin markers (142,146 SNPs) was constructed based on cowpea F2 population using re-sequencing technology. The map consisted of 11 linkage groups with a total length of 1333.48 cM and an average map spacing of 0.45 cM. The length of different linkage groups ranged from 84.63 cM to 183.15 cM, and the average plot distance ranged from 0.27 cM to 0.89 cM. A total of 15 QTLs were detected to be associated with 14 traits, including 100-grain weight, flower color, pod length, pod shape, pod shape and grain color, respectively. One major QTL region was detected for pod type, pod length, and number of branches per main stem, and multiple QTLs regions were detected for other traits. Candidate genes related to pod length, number of pods per plant, and single/double color of grains were further identified by gene annotation analysis in the interval. The results of QTL analysis in this study will lay a foundation for marker-assisted selection of important traits of cowpea, and candidate gene screening will help to further analyze the genetic mechanism of these traits and improve the level of molecular genetics research of cowpea.

Key words: cowpea, SNP, genetic map, agronomic traits, QTL mapping

Table 1

Parental traits for cowpea mapping population"

质量性状
Quality trait		 亲本 Parent 标准差
SD		 显著性差异检测Significant test
PGIP14 优冠 Youguan
荚质Pod type 硬荚Hard pod 软荚Soft pod — —
籽粒颜色构成Type of seed color 单Single 单Single — —
花色Flower color 白White 紫Purple — —
脐环色有无Presence or absence of hilum color 有Present 无Absent — —
粒色Seed color 白White 红Red — —
荚形Pod shape 圆筒形Cylinder 长圆条形Long cylinder — —
荚色 Pod color 紫色Purple 绿色Green — —
荚长Pod length 14 73 29.5** P < 0.01
主茎分枝数Number of branches per stem 6 12 3* P < 0.05
单株荚数Number of pods per plant 16 21 2.5* P < 0.05
单荚粒数Number of seeds per pod 12 16 2 P > 0.05
籽粒分布密度Seed density 0.86 0.22 0.32* P < 0.05
百粒重Hundred-grain weight 18 30 6* P < 0.05

Table 2

Frequency of Distribution on quality traits in F2 and F3 populations of cowpea"

性状
Quality trait		 变异类型
Variation types		 分布频率Frequency of distribution (%)
F2 F3
荚质Pod type 硬荚Hard pod 92.7 44.3
软荚Soft pod 7.3 55.7
籽粒颜色构成Type of seed color 单Single 79.2 37.5
双Double 20.8 14.1
杂合Heterozygous 48.4
花色Flower color 紫色Purple 75.5 38.5
白色White 24.5 18.2
浅紫Light purple 43.2
脐环色有无Presence or absence of hilum color 有Present 39.6 75.5
无Absent 60.4 24.5
粒色Seed color 深色系Dark color 76.0 72.4
浅色系Light color 24.0 27.6
荚形Pod shape 圆筒形Cylinder 40.6 7.3
长圆筒形Long cylinder 59.4 45.8
杂合Heterozygous 46.9
荚色Pod color 紫色Purple 58.9 79.7
绿色Green 41.1 20.3

Table 3

Distribution of quantitative traits in F2 and F3 populations of cowpea"

性状
Trait		 F2 F3
变异范围
Range of variation		 平均
Mean
value		 变异系数
Variable
coefficient (%)		 变异范围
Range of variation		 平均
Mean value		 变异系数
Variable
coefficient (%)
百粒重Hundred-grain weight (g) 11.3-31.3 20.0 21.56 11.4-28.5 19.7 19.61
荚长Pod length (cm) 11.6-55.2 32.4 25.83 14.4-51.3 27.6 23.97
主茎分枝数Number of branches per main stem 2-12 6.9 24.60 2-13 6.8 25.28
单株荚数Number of pods per plant 2-26 12.2 45.89 2-30 14.2 48.40
单荚粒数Number of seeds per pod 3-16 9.0 25.70 3-18 9.2 25.62
籽粒分布密度Seed density 0.13-0.90 0.40 34.40 0.14-0.80 0.35 35.93

Table 4

Basic information of a high density map for cowpea"

染色体
Chromosome		 SNP数量
Number of SNP		 Bin标记数
Number of bin marker		 总遗传距离
Total distance
(cM)		 平均遗传距离
Average distance (cM)		 最大
Max. gap
(cM)
1 4689 184 93.68 0.51 3.53
2 9661 190 84.63 0.45 3.16
3 27,206 502 137.76 0.27 6.99
4 4231 146 129.47 0.89 5.41
5 10,175 280 130.46 0.47 4.05
6 14,727 193 103.91 0.54 7.36
7 9362 193 100.75 0.52 3.22
8 13,572 286 111.80 0.39 3.48
9 10,277 298 136.10 0.46 2.96
10 8552 293 183.15 0.63 10.73
11 29,694 419 121.57 0.29 2.33
总计Total 142,146 2984 1333.28 0.45 10.73

Table 5

QTLs mapping of agronomic traits in cowpea"

性状
Trait		 位点
QTL		 染色体
Chr.		 起始位置
Start		 终止位置
End		 加性效应
ADD		 显性效应
DOM		 贡献率
PVE (%)
荚质Pod type qPt1** 1 13.848 14.108 -0.107 0.148 21.753
荚长Pod length qPL1 3 54.012 54.530 3.563 -1.498 14.666
qPL2* 5 69.084 69.602 2.886 -0.486 7.032
主茎分枝数
Number of branches per stem		 qNuBS1** 5 37.989 37.989 -0.492 -0.206 1.488
籽粒颜色构成
Type of seed color		 qTSC1 9 62.767 63.285 -0.340 -0.336 9.650
qTSC2 7 67.061 67.320 0.088 0.231 4.301
花色
Flower color		 qFC1 7 53.328# 53.587 0.394 0.276 10.790
qFC2** 7 50.738 50.997 0.350 0.261 8.180
脐环色有无
Presence or absence of hilum color		 qPAHC1 7 53.328# 53.587 -0.365 -0.313 7.342
粒色
Seed color		 qSC1** 7 52.551 52.810 2.877 2.532 13.780
qSC2* 5 19.178 19.437 0.621 -0.662 25.802
qSC3* 9 57.478 57.737 -0.375 -0.530 2.036
单株荚数Pods per plant qPP1 8 107.550 107.809 -1.728 -1.902 1.368
单荚粒数Seeds per pod qSP1 8 108.327## 108.586 -0.965 -1.579 4.818
荚形Pod shape qPS1 8 108.327## 108.586 0.256 0.266 3.906
籽粒分布密度Seed density qSD1** 8 108.327## 108.586 0.816 0.752 5.011
百粒重Hundred-grain weight qSW1 8 108.327## 108.586 3.471 2.837 7.784
成熟期Mature period qMP1** 10 160.246 160.505 -2.375 -0.958 2.408
荚色Pod color qPC1 11 53.997 54.256 -0.602 0.409 48.682

Table S1

52 non-synonymous mutant genes detected within different QTLs related with agronomic traits in cow pea"

染色体
Chr.		 基因ID
Gene ID		 QTL区间
QTL interval		 基因区间
Genetic interval		 基因功能注释
Gene function annotation
3 LOC114178564 54.012-54.53 26659350-26665086 protein WVD2-like 7
3 LOC114175233 54.012-54.53 26678051-26680075 probable aquaporin NIP-type
5 LOC114184079 37.989-37.989 8952543-8954607 CASP-like protein 4B1
5 LOC114185628 37.989-37.989 8960120-8961928 soyasapogenol B glucuronide galactosyltransferase-like
5 LOC114184299 37.989-37.989 8963524-8965966 soyasapogenol B glucuronide galactosyltransferase-like
5 LOC114183879 37.989-37.989 8966609-8968346 soyasapogenol B glucuronide galactosyltransferase-like
5 LOC114183944 37.989-37.989 8973763-8975587 soyasapogenol B glucuronide galactosyltransferase-like
5 LOC114183315 37.989-37.989 8978158-8978658 uncharacterized LOC114183315
5 LOC114184286 37.989-37.989 8982079-8983730 soyasapogenol B glucuronide galactosyltransferase-like
5 LOC114184106 37.989-37.989 8987736-8989630 soyasapogenol B glucuronide galactosyltransferase-like
5 LOC114183319 37.989-37.989 8993599-8994730 uncharacterized LOC114183319
5 LOC114183325 37.989-37.989 8995420-8996926 protein MAIN-LIKE 1-like
染色体
Chr.		 基因ID
Gene ID		 QTL区间
QTL interval		 基因区间
Genetic interval		 基因功能注释
Gene function annotation
5 LOC114185420 37.989-37.989 9039186-9042595 probable protein phosphatase 2C 65
5 LOC114183906 37.989-37.989 9052366-9054961 patellin-6-like
5 LOC114183956 37.989-37.989 9058059-9060862 pentatricopeptide repeat-containing protein At3g18020
5 LOC114184027 37.989-37.989 9064413-9065319 dirigent protein 22-like
5 LOC114184026 37.989-37.989 9078035-9084744 kelch-like protein 12
5 LOC114184321 37.989-37.989 9098800-9100029 F-box/kelch-repeat protein At3g23880-like
5 LOC114183366 37.989-37.989 9102509-9110139 protein SIEL
7 LOC114191246 50.738-50.997 18194589-18195465 protein FAR1-RELATED SEQUENCE 5-like
7 LOC114191250 50.738-50.997 18272456-18273566 protein MAIN-LIKE 1-like
7 LOC114190940 50.738-50.997 18288489-18290111 cytochrome P450 94A2-like
7 LOC114189521 50.738-50.997 18327604-18332035 probable myosin-binding protein 4
7 LOC114192004 50.738-50.997 18415284-18420952 fructokinase-1
7 LOC114191022 50.738-50.997 18636639-18638015 histone H1-like
7 LOC114189590 52.551-52.810 19451491-19452509 calmodulin-like protein 11
7 LOC114189868 52.551-52.810 19575072-19579311 protein indeterminate-domain 12-like
7 LOC114192564 53.328-53.587 19713195-19721744 VAN3-binding protein-like
7 LOC114192741 53.328-53.587 19735070-19741228 serine/threonine-protein kinase Nek2-like
7 LOC114190506 53.328-53.587 19953568-19958537 type I inositol polyphosphate 5-phosphatase 4-like
7 LOC114189546 67.061-67.320 24405575-24410854 flap endonuclease 1
8 LOC114194067 108.327-108.586 37576701-37580094 uncharacterized LOC114194067
8 LOC114193981 108.327-108.586 37582007-37593015 uncharacterized LOC114193981
8 LOC114195189 108.327-108.586 37602436-37608479 disease resistance protein SUMM2-like
8 LOC114195190 108.327-108.586 37614877-37621041 probable disease resistance protein At1g61180
8 LOC114195691 108.327-108.586 37627795-37655794 uncharacterized LOC114195691
8 LOC114194109 108.327-108.586 37666847-37673621 nuclear pore complex protein NUP133
8 LOC114194567 108.327-108.586 37679572-37683878 photosystem II stability/assembly factor HCF136, chloroplastic-like
8 LOC114193937 108.327-108.586 37693871-37694732 uncharacterized LOC114193937
8 LOC114194173 108.327-108.586 37707580-37710446 OBERON-like protein
8 LOC114195292 108.327-108.586 37724791-37734006 histidine kinase 2
8 LOC114193675 107.55-107.809 37231477-37234638 probable L-type lectin-domain containing receptor kinase S.7
8 LOC114193834 107.55-107.809 37251133-37255531 cellulose synthase-like protein E1
8 LOC114193715 107.55-107.809 37267920-37275855 cellulose synthase-like protein E6
8 LOC114194540 107.55-107.809 37286246-37289537 WEB family protein At5g55860-like
8 LOC114194521 107.55-107.809 37290983-37293883 uncharacterized LOC114194521
8 LOC114194615 107.55-107.809 37314388-37317944 oligopeptide transporter 1-like
9 LOC114196343 57.478-57.737 30208037-30209581 protein TRANSPARENT TESTA GLABRA 1
10 LOC114167141 160.246-160.505 35924191-35935677 proline-, glutamic acid- and leucine-rich protein 1
10 LOC114167157 160.246-160.505 35940037-35947146 mediator of RNA polymerase II transcription subunit 19a
10 LOC114166573 160.246-160.505 35969561-35974234 formin-like protein 1
11 LOC114168914 53.997-54.256 28652619-28654392 probable O-methyltransferase 3
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