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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (01): 9-19.doi: 10.3724/SP.J.1006.2020.94056

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

Mapping of QTLs for leafstalk angle in soybean

WANG Cun-Hu,LIU Dong,XU Rui-Neng,YANG Yong-Qing(),LIAO Hong   

  1. College of Resources and Environment, Fujian Agriculture and Forestry University/Root Biology Center, Fuzhou 350002, Fujian, China
  • Received:2019-04-12 Accepted:2019-08-09 Online:2020-01-12 Published:2019-09-12
  • Contact: Yong-Qing YANG E-mail:yyq287346@163.com
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31830083);Science and Technology Innovation Fund of Fujian Agriculture and Forestry University(CXZX2018028)

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Abstract:

Leafstalk angle is one of the most important elements for shoot architecture of soybean, affecting canopy architecture, photosynthetic efficiency and final grain yield. Exploring genetic basis of soybean leafstalk angle is significant to improve soybean yield. In this study, two soybean accessions BLA and SLA, contrasting in leafstalk angle, and their derived RIL population were used for high resolution genetic map construction and QTL detection for leafstalk angle, further the near-isogenic lines (NIL) were constructed to validate partial QTLs. Genetic analysis results showed that values of leafstalk angle performed serial and normal distribution which coincides with genetic characteristics of quantitative traits. Additionally, a high resolution genetic map consisting of 859 bin markers was constructed by using GBS method. The linkage map covered 2326.9 cM of genetic distance and the average distance between two markers was 2.763 cM. A total of 14 QTLs for regulating leafstalk angle were detected, with explained 6.9%-12.4% of genetic variation, and their LOD values varied from 2.58 to 4.80, and five of them were clustered together on Chromosome 12. The phenotype of the NILs for qLA12 and qLA18 revealed that leafstalk angle performed significant difference between same pair of NILs which strongly suggested that qLA12 and qLA18 are two believable QTLs. In summary, our results lay a foundation for cloning functional genes of regulating leafstalk angle and provide genetic resources for breeding elite soybean varieties with ideal shoot architecture.

Key words: soybean shoot architecture, leafstalk angle, QTL mapping, near-isogenic lines (NIL)

Fig. 1

Phenotypic differences in leafstalk angle between parents (A) and statistical analysis (B) BLA: big leafstalk angle; SLA: small leafstalk angle. ** indicate the significant differences of leaf petiole angle between SLA and BLA at the 1% probability level. LA-H, LA-M, and LA-L represent angles of high (H), middle (M), and low (L) leaves petiole, respectively."

Table 1

Phenotypic variation and genetic analysis of leafstalk angle traits in soybean RILs"

性状
Trait		 亲本Parents 重组自交系群体RILs 遗传力
h2b
BLA±SE SLA±SE 均值 Mean 标准差SD 变异系数
CV (%)		 最小值Min. 最大值Max. 峰度
Skew.		 偏度
Kurt.
LA-H 36.60±1.36 36.60±2.72 37.25 6.57 17.64 20 75 0.78 2.29 0.70
LA-M 53.30±1.36 51.67±3.60 56.61 8.82 15.58 30 85 0.56 0.52 0.72
LA-L 95.00±2.36 73.30±2.72 74.83 12.17 16.26 20 110 -1.22 3.16 0.90

Table 2

Summary of bin marker characteristics of recombinant inbred line population"

染色体
Chr.		 遗传距离
Genetic distance (cM)		 物理长度
Physical length		 标记数量
Number of bin markers		 平均覆盖距离
Average coverage distance (cM)
Chr01 132.25 56,510,449 45 2.94
Chr02 149.48 47,706,575 39 3.83
Chr03 82.60 45,730,193 38 2.17
Chr04 125.97 51,405,255 50 2.52
Chr05 99.11 41,919,006 34 2.91
Chr06 128.98 50,892,625 44 2.93
Chr07 113.88 43,534,570 44 2.59
Chr08 166.04 47,709,553 45 3.69
Chr09 157.61 50,173,153 32 4.93
Chr10 85.61 51,542,279 25 3.42
Chr11 158.21 34,671,664 53 2.99
Chr12 123.75 40,030,102 47 2.63
Chr13 135.19 45,514,498 45 3.00
Chr14 87.35 47,841,279 44 1.99
Chr15 106.51 51,710,377 48 2.22
Chr16 74.30 37,192,783 46 1.62
Chr17 90.05 41,348,852 45 2.00
Chr18 113.71 57,961,359 46 2.47
Chr19 103.79 50,522,110 46 2.26
Chr20 92.53 47,868,276 43 2.15
合计Total 2326.90 941,784,958 859 55.26

Fig. 2

High resolution genetic map The left scale represents the genetic distance, and the different colors on the linkage group indicate the marker density."

Table 3

Putative QTLs for leafstalk angle traits in soybean RILs in the field"

性状
Trait		 QTL 染色体
Chr.		 标记区间
Markers interval		 遗传位置
Genetic position (cM)		 LOD 加性效应Add 表型变异PVE (%)
上位
LA-H		 qLA12a Gm12 Chr12.3021337-Chr12.4783251 20.466 3.55 1.76 9.3
qLA12b Gm12 Chr12.6175142-Chr12.6947560 32.213 3.43 1.61 9.0
qLA12c Gm12 Chr12.2086945-Chr12.2529118 7.231 2.70 1.46 7.2
qLA01 Gm01 Chr01.55523848-Chr01.56419281 131.054 3.85 -1.67 10.1
qLA11 Gm11 Chr11.10213098-Chr11.24373759 57.808 2.58 1.55 6.9
中位LA-M qLA09 Gm09 Chr09.4074635-Chr09.4606081 34.147 3.97 -2.36 10.4
qLA12d Gm12 Chr12.1868502-Chr12.2529118 6.231 3.86 2.30 10.1
qLA12a Gm12 Chr12.3021337-Chr12.4783251 17.466 3.19 2.33 8.4
qLA14 Gm14 Chr14.6976251-Chr14.43836321 60.580 2.70 -2.70 7.2
qLA17 Gm17 Chr17.37570037-Chr17.36696957 49.792 2.62 -1.87 7.0
下位LA-L qLA18 Gm18 Chr18.46032220-Chr18.47375074 63.343 4.80 3.98 12.4
qLA06 Gm06 Chr06.11495976-Chr06.15321801 70.098 4.21 -4.69 11.0
qLA15 Gm15 Chr15.11748320-Chr15.47611763 83.523 2.94 -3.20 7.8
qLA07 Gm07 Chr07.7016819-Chr07.8103486 29.912 2.71 3.02 7.2

Table 4

dCAPS markers used in this study"

引物编号
Primer name		 SNP位点
SNP loci		 内切酶
Enzyme		 引物序列
Primer sequence (5°-3°)		 预期片段大小
Expected product size (bp)
dCAPS-Chr12-1 3465298 Spe I F: AGTGCTAAAAACAATCCCCG 250/(226+24)
R: GAGCCCGAATGAAGTGGGTGAGGACTAG
dCAPS-Chr12-2 3513670 Bsm I F: GCATAGCCTCTCCAATCCAT 229/(198+31)
R: GCATTTGAATGAAGACTTGTGGAGGAATG
dCAPS-Chr12-3 3577958 Bmr I F: CTGAGGATGTGATCCTGAGAAATGCTACTG 194/(161+33)
R: CTCCACCCATCATCAAAATA
dCAPS-Chr12-4 3593743 Acl I F: TGCCAACATTCCCTCATCAG 186/(160+26)
R: TTAGATGAAGCAAATGATTCAAATAACGT
dCAPS-Chr12-5 3953314 SnaB I F: CTTAAACCACCCGGTGTCTCTTGCGGTACG 234/(205+29)
R: GTGTGTTACTATCTCTCTCT
dCAPS-Chr12-6 4183623 Bsm I F: GGAAACTTGGTTAATAGCTAAGATCCTTGA 215/(183+32)
R: GATTGGAGGAAAGTGGAAGA
dCAPS-Chr12-7 4546007 Sma I F: ACTCCCTTCTTGTTGCCTTG 169/(141+28)
R: AATTGCTTGATAAGGTCCTGCTAGGCCCG
dCAPS-Chr18-1 45231954 Taq I F: CTCTCATCTCAAACAAGTCT 209/(181+28)
R: GAGTTAATCCTAGTTTAAAATGTCATTTCG
dCAPS-Chr18-2 46986384 Sna I F: GAAGTAACAACAGACTACGACGGTTGTAT 230/(205+25)
R: CTAAGACGGACCTACAAAGC
dCAPS-Chr18-3 47034338 Asu I F: GTAGACACCGGCGATCGGGGACTTTGGTC 204/(181+23)
R: CAGCAAGTCCACCAGCATCT
引物编号
Primer name		 SNP位点
SNP loci		 内切酶
Enzyme		 引物序列
Primer sequence (5°-3°)		 预期片段大小
Expected product size (bp)
dCAPS-Chr18-4 48080921 Taq II F: GTCGTGAAATTTGAGCACCACGTTCGCCA 247/(221+26)
R: TATCTCGCAAATCCCAACGT
dCAPS-Chr18-5 48514645 Mnl I F: TGGTTGTTCTGTTTTTCTTTGTTCTACCT 244/(215+29)
R: GTCGACTTCTATCTACAAAC
dCAPS-Chr18-6 50618122 Xmn I F: CTATACTCGGTCACTTATTG 195/(167+28)
R: CTTCTTAGTAACCCTTTCCAAGTGAAAACA
dCAPS-Chr18-7 51595218 Dpn I F: GGTCACGTTGTTTTGTAAGAATGTTCCGA 242/(213+29)
R: AACCACAAGCGTAATGAGAT

Fig. 3

Phenotypic differences in leafstalk angle between near isogenic lines qLA12 (A) and statistical analysis (B) The consistent yellow alphabet on the pots indicates a pair of isogenic line from the same F5:6 family. The red box and curved arrows indicate the observed location."

Fig. 4

Phenotypic differences in leafstalk angle between near isogenic lines qLA18 (A) and statistical analysis (B) The consistent yellow alphabet on the pots indicates a pair of isogenic line from the same F5:6 family. The red box and curved arrows indicate the observed location."

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