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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (11): 1667-1677.doi: 10.3724/SP.J.1006.2020.04043


Development of molecular markers and fine mapping of qBN-18 locus related to branch number in soybean (Glycine max L.)

WU Hai-Tao1,3(), ZHANG Yong2, SU Bo-Hong1,3, Lamlom F Sobhi3,4, QIU Li-Juan3,*()   

  1. 1 College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
    2 Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161606, Heilongjiang, China
    3 National Key Facility for Gene Resources and Genetic Improvement / Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    4 Plant Production Department, Faculty of Agriculture Saba Basha, Alexandria University, Alexandria, Egypt
  • Received:2020-02-25 Accepted:2020-06-02 Online:2020-11-12 Published:2020-06-22
  • Contact: Li-Juan QIU E-mail:1960478192@qq.com;qiulijuan@caas.cn
  • Supported by:
    The study was supported by the National Key Research and Development Program of China(2016YFD0100201);the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences, and the Protection and Utilization of Soybean Germplasm Resources(2019NWB036-05)


The branch number is one of the important factors influencing soybean yield, which is directly related to pod setting rate. At the same time, it is also an important component of soybean plant type, and further affects the yield by adjusting the population structure and planting density. At present, there is few report related to map-based cloning of genes related to branch number. Therefore, the discovery of genes/QTL involved in the regulation of soybean branching is of great significance for the basic research on the establishment of plant type and the applied research on the development of high-yielding varieties. In this study, based on the F2 of crossing low-branched variety Kenfeng 19 (KF19) and high-branched variety Kennong 24 (KN24), we developed the F7:8 recombinant inbred line (RIL) population, consisting of 606 lines, and two backcrossing populations consisting of 1486 individuals for KF19-BC3F2 and 1150 individuals for KN24-BC2F2. Within the localization interval of the new QTL of the branch number of chromosome 18 (qBN-18), 11 polymorphism SSR markers were screened out to identify the RIL population, and region of qBN-18 was reduced from 1.6 Mb to 113 kb. After developing two InDel markers BR69 and BR77 in the mapping region, the backcross population was used to screen the exchange individuals, the interval of qBN-18 was further reduced to 63.7 kb, including 9 genes. Those results provide the information for gene map-based cloning and molecular marker assisted breeding of branch number in soybean.

Key words: soybean, branch number, QTL mapping, candidate genes

Table 1

Molecular markers information for fine mapping"

Primer name
Physical position (bp)
Forward primer (5'-3')
Reverse primer (5'-3')

Table 2

Positions of two InDel markers, the primers and the expected length of the amplified fragment"

Primer name
position (bp)
Forward primer (5'-3')
Reverse primer (5'-3')
片段长度Product size (bp)
Kennong 24
Kenfeng 19

Fig. 1

Identification of branch numbers in KF19, KN24 and the population A: parent plant; B-C: KN24 and KF19 branch number phenotypes in 2018 and 2019, respectively; D-E: histogram of frequency distribution of F7 and F7:8 branch numbers, respectively; F: histogram of the frequency distribution of branch number F2 in the backcross population in 2018. Mean value and standard deviation of parental phenotypes are indicated by vertical dotted lines. Curve represents density plot. ***: P < 0.001."

Table 3

Descriptive statistics of branch number (BN) in parental lines of KN24 and KF19 and their populations of F7, F7:8 in 2018 and 2019"

Mean±SD of BN
Parameters of BN in populations
KN24 KF19 平均值±标准差
2018 5.5±1.0 0.5±0.5 4.5±1.9 0-10 0.2740 -0.3887
2019 6.8±1.2 0.7±0.6 3.4±1.5 0-8 0.3390 -0.5720

Fig. 2

Branch number QTL qBN-18 of soybean chromosome 18 was located by the RIL populations consisted of KF19 and KN24"

Table 4

Branch number QTLS identified in the F7:8 population of KF19 ×KN24"

Marker interval
Physical position of
interval (bp, Wm82.a2.v1)
LOD value
PVE (%)
Additive effect
F7:8 18 BARCSOYSSR_18_1834-BARCSOYSSR_18_1841 55,877,756-55,990,750 19.33 14.24 0.75

Fig. 3

Correlation analysis between genotype and phenotypic by BR69 and BR77 markers in RIL population A: correlation analysis between genotype and phenotype of BR69; B: correlation analysis between genotype and phenotype of BR77. The abscissa is the genotype, the multiple branches are denoted as a, the few branches are denoted as b, and the vertical ordinate is the number of branches. ***P < 0.001."

Fig. 4

Validation of qBN-18 locus A: qBN-18 loci between marker BARCSOYSSR_18_1777 and BARCSOYSSR_18_1875 was identified using 1486 individuals of KF19-BC3F2 and 1150 individuals of KN24-BC2F2; B: BARCSOYSSR_18_1791, BARCSOYSSR_18_1803, BARCSOYSSR_18_1827 and BARCSOYSSR_18_1856 were used to identify 568 recombinant strains between BARCSOYSSR_18_1777 and BARCSOYSSR_18_1875; C: qBN-18 is located between tag BR69 and tag BR77. H: heterozygous genotype."

Table 5

Homologous genes and gene annotation of genes in the location interval"

Homologous gene
Gene annotation
Glyma.18g276900 AT5G11390.1 WPP domain-interacting protein 1
Glyma.18g277000 AT3G02030.1 Pentatricopeptide repeat (PPR) superfamily protein
Glyma.18g277100 AT3G30530.1 Basic leucine-zipper 42
Glyma.18g277300 AT3G02060.1 6-phosphogluconate dehydrogenase family protein
Glyma.18g277600 AT4G25760.1 Glutamine dumper 2
Glyma.18g277700 AT4G15733.1 SCR-like 11

Fig. 5

Expression profiles of nine genes by Phytozome v12.1"

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