Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (3): 565-571.doi: 10.3724/SP.J.1006.2022.14011


Improving seed number per pod of soybean by molecular breeding based on Ln locus

DU Hao1(), CHENG Yu-Han2, LI Tai1, HOU Zhi-Hong1, LI Yong-Li1, NAN Hai-Yang1, DONG Li-Dong1, LIU Bao-Hui1, CHENG Qun1,*()   

  1. 1School of Life Sciences, Guangzhou University, Guangzhou 510006, Guangdong, China
    2Beijing International Urban Agricultural Science and Technology Park, Zhong-Nong-Fu-Tong, Beijng 100083, China
  • Received:2021-01-19 Accepted:2021-06-16 Online:2022-03-12 Published:2021-07-13
  • Contact: CHENG Qun E-mail:duhao990303@163.com;chengqun0118@gzhu.edu.cn
  • Supported by:
    National Natural Science Foundation of China(32001508);National Natural Science Foundation of China(31930083);National Natural Science Foundation of China(31801384)


Molecular design breeding is one of the important methods to combine molecular genetics with conventional breeding, and to breed a series soybean variety with excellent traits. Although this method can shorten the breeding process to a large extent, it is rarely used in the artificial breeding process. Increasing production is one of the most important goals in the process of soybean breeding. Soybean is a typical short-day bean plant, which provides more than a quarter of plant protein for human and animals in the world. In the process of soybean breeding, increasing the yield is one of the main breeding objectives, among which the number of seeds per pod is one of the key traits to determine the yield per plant. In soybean, the number of seeds per pod was positively correlated with leaf shape, which was controlled by an allele Ln/ln. The broad leaflet (Ln) usually linked with no 4-seed pod, and narrow leaflet (ln) associated with 4-seed pod. Although Ln was potentially important for soybean yield, whether this locus could be used in molecular breeding had not been reported. In this study, we found that the narrow leaflet variety was always in high latitude, and the broad leaflet variety in low latitude. To improve soybean yield in low latitude, we developed the molecular marker of Ln. ln was substituted into broad leaflet varieties Willams 82 and Huaxia 3 by backcrossing. Our data provide an important theoretical and practical basis for molecular design breeding to improve soybean yield.

Key words: soybean, Ln, yield, the number of seeds per pod, molecular design

Fig. 1

Geographical distribution of different alleles of Ln variation A: the geographical distribution of Ln variation in China, red for Ln, blue for ln; B: the allele frequency of Ln in different regions. HR: Huanghuai region; NR: Northern region; SR: Southern region; NE: Northeast region."

Fig. 2

Leaf phenotypes of different soybean varieties A: the phenotype of DN50, SN14, HH43, SN88 leaves, the yellow lines represent the leaf width and the red lines represent the leaf length; B: the phenotype of HX3, HX5, BR21, and W82 leaves; bar: 1 cm; C: the length-width ratio of different leaves."

Table 1

Number of pod from 1-seed to 5-seed"

1-seed pod number
2-seed pod number
3-seed pod number
4-seed pod number
5-seed pod number
DN50 6±0.33 12±0.25 23±0.19 25±0.08 0
SN14 9±0.23 15±0.24 20±0.26 25±0.16 0
HH43 11±0.33 15±0.19 28±0.32 29±0.45 1±0.94
SN88 5±0.14 14±0.27 23±0.35 26±0.12 0
HX3 16±0.12 60±0.44 35±0.28 0 0
HX5 22±0.34 54±0.41 34±0.42 0 0
BR21 24±0.12 43±0.25 59±0.34 0 0
W82 18±0.32 39±0.32 61±0.83 2±0.88 0

Fig. 3

Electrophoresis of molecular makers of Ln A: the detection results of Ln. M: DL2000 maker; 1: the digested product of Ln; 2: the digested product of ln; 3: the digested product of Ln heterozygous. B: The genotype of Ln in different cultivars. 1-4: HX3, HX5, BR21, and W82; 5-8: DN50, SN14, HH43, and SN88; 9: the genotype of hybrid between W82 and HH43; 10: the genotype of hybrid between HX3 and HH43."

Fig. 4

Phenotype of ln mutant A: the phenotype of W82 and W82-ln leaves; B: leaves length-width ratio of W82 and W82-ln; C: the phenotype of HX3 and HX3-ln leaves; D: leaves length-width ratio of HX3 and HX3-ln; E: pod types occurring in W82 and W82-ln and pod types occurring in HX3 and HX3-ln, * represents the main type of pod number in the variety; F: total pod number of W82 and W82-ln; G: 4-seed pod number of W82 and W82-ln; H: grain weight per plant of W82 and W82-ln; I: total pod number of HX3 and HX3-ln; J: 4-seed pod number of HX3 and HX3-ln; K: grain weight per plant of HX3 and HX3-ln. **: P < 0.01."

[1] Ashraf M, Foolad R. Crop breeding for salt tolerance in the era of molecular markers and marker-assisted selection. Plant Breed, 2013, 132:10-20.
doi: 10.1111/pbr.2013.132.issue-1
[2] Sharma S, Sharma A. Molecular markers based plant breeding. Adv Res, 2018, 16:2348.
[3] Hartung R C, Specht J E, Williams J H. Modification of soybean plant architecture by genes for stem growth habit and maturity. Crop Sci, 1981, 21:51-62.
doi: 10.2135/cropsci1981.0011183X002100010015x
[4] 田志喜, 刘宝辉, 杨艳萍, 李明, 姚远, 任小波, 薛勇彪. 大豆分子设计育种成果与展望. 中国科学院院刊, 2018, 33:915-922.
Tian Z X, Liu B H, Yang Y P, Li M, Yao Y, Ren X B, Xue Y B. Update and prospect of soybean molecular module-based designer breeding in China. Bull Chin Acad Sci, 2018, 33:915-922 (in Chinese with English abstract).
[5] Cheng Q, Dong L D, Su T, Li T Y, Gan Z R, Nan H Y, Lu S J, Fang C, Kong L P, Li H Y, Hou Z H, Kou K, Tang Y, Lin X Y, Zhao X H, Chen L Y, Liu B H, Kong F J. CRISPR/Cas9-mediated targeted mutagenesis of GmLHY genes alters plant height and internode length in soybean. BMC Plant Biol, 2019, 19:562.
doi: 10.1186/s12870-019-2145-8 pmid: 31852439
[6] Chen L Y, Nan H Y, Kong L P, Yue L, Yang H, Zhao Q S, Fang C, Li H Y, Cheng Q, Lu S J, Kong F J, Liu B H, Dong L D. Soybean AP1 homologs control flowering time and plant height. J Integr Plant Biol, 2020, 62:1868-1879.
doi: 10.1111/jipb.v62.12
[7] Fan C C, Xing Y Z, Mao H L, Lu T T, Han B, Xu C G, Li X H, Zhang Q F. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet, 2006, 112:1164-1171.
doi: 10.1007/s00122-006-0218-1
[8] Lu S J, Dong L D, Fang C, Liu S L, Kong L P, Cheng Q, Chen L Y, Su T, Nan H Y, Zhang D, Zhang L, Wang Z J, Yang Y Q, Yu D Y, Liu X L, Yang Q Y, Lin X Y, Tang Y, Zhao X H, Yang X Q, Tian C E, Xie Q G, Li X, Yuan X H, Tian Z X, Liu B H, Weller J L, Kong F J. Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nat Genet, 2020, 52:428-436.
doi: 10.1038/s41588-020-0604-7
[9] Kong F J, Liu B H, Xia Z J, Sato S, Kim B M, Watanabe S, Yamada T, Tabata S, Kanazawa A, Harada K, Abe J. Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the control of photoperiodic flowering in soybean. Plant Physiol, 2010, 154:1220-1231.
doi: 10.1104/pp.110.160796
[10] Li Z B, Cheng Q, Gan Z R, Hou Z H, Zhang Y H, Li Y L, Li H Y, Nan H Y, Yang C, Chen L N, Lu S J, Shi W Q, Chen L Y, Wang Y P, Fang C, Kong L P, Su T, Li S C, Kou K, Wang L S, Kong F J, Liu B H, Dong L D. Multiplex CRISPR/Cas9-mediated knockout of soybean LNK2 advances flowering time. Crop J, 2021, 9:767-776.
doi: 10.1016/j.cj.2020.09.005
[11] Li M W, Liu W, Lam H M, Gendron J M. PRR3 genes during soybean domestication PRR3 genes during soybean domestication. Plant Cell Physiol, 2019, 60:407-420.
doi: 10.1093/pcp/pcy215
[12] Cheng Q, Gan Z R, Wang Y P, Lu S J, Hou Z H, Li H Y, Xiang H T, Liu B H, Kong F J, Dong L D. J contributes to salt stress tolerance by up-regulating salt-responsive genes J contributes to salt stress tolerance by up-regulating salt-responsive genes. Front Plant Sci, 2020, 11:272.
doi: 10.3389/fpls.2020.00272 pmid: 32256507
[13] Hymowitz T. On the domestication of the soybean. Econ Bot, 1970, 24:408-421.
doi: 10.1007/BF02860745
[14] Lee G A, Crawford G W, Liu L, Sasaki Y, Chen X. Archaeological soybean (Glycine max) in East Asia: does size matter? PLoS One, 2011, 6:e26720.
doi: 10.1371/journal.pone.0026720
[15] Fang C, Li W Y, Li G Q, Wang Z, Zhou Z K, Ma Y M, Shen Y I, Li C C, Wu Y H, Zhu B G, Yang W C, Tian Z X. Ln gene through combined approach of map-based cloning and association study in soybean Ln gene through combined approach of map-based cloning and association study in soybean. J Genet Genomics, 2013, 40:93-96.
doi: 10.1016/j.jgg.2013.01.002
[16] Jeong N, Moon J J, Kim H S, Kim C G, Jeong S C. Fine genetic mapping of the genomic region controlling leaflet shape and number of seeds per pod in the soybean. Theor Appl Genet, 2011, 122:865-874.
doi: 10.1007/s00122-010-1492-5
[17] Jeong N, Suh S J, Kim M H, Lee S, Moon J K, Kim H S, Jeong S C. Ln is a key regulator of leaflet shape and number of seeds per pod in soybean. Plant Cell, 2012, 24:4807-4818.
doi: 10.1105/tpc.112.104968
[18] Sayama T, Tanabata T, Saruta M, Yamada T, Anai T, Kaga A, Ishimoto M. Ln gene in induced soybean mutants Ln gene in induced soybean mutants. Breed Sci, 2017, 67:363-369.
doi: 10.1270/jsbbs.16201
[19] Ohno C K, Reddy G V, Heisler M G, Meyerowitz E M. Arabidopsis JAGGED gene encodes a zinc finger protein that promotes leaf tissue development Arabidopsis JAGGED gene encodes a zinc finger protein that promotes leaf tissue development. Development, 2004, 131:1111-1122.
doi: 10.1242/dev.00991
[20] Neumaier N, James A T. Exploiting the long-juvenile trait to improve adaptation of soybeans to the tropics. Food Legume Newsl, 1993, 8:12-14.
[21] Spehar C R. Impact of strategic genes in soybean on agricultural development in the Brazilian tropical savannah. Field Crops Res, 1995, 41:141-146.
doi: 10.1016/0378-4290(95)00007-D
[22] Fang C, Ma Y M, Wu S W, Liu Z, Wang Z, Yang R, Hu G H, Zhou Z K, Yu H, Zhang M, Pan Y, Zhou G A, Ren H X, Du W G, Yan H R, Wang Y P, Han D Z, Shen Y T, Liu S L, Liu T F, Zhang J X, Qin H, Yuan J, Yuan X H, Kong F J, Liu B H, Li J Y, Zhang Z W, Wang G D, Zhu B G, Tian Z X. Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome Biol, 2017, 18:161-175.
doi: 10.1186/s13059-017-1289-9
[23] Wu F Q, Kang X H, Wang M L, Haider W, Price W B, Hajek B, Hanzawa Y. GmCOL1 feed-forward loop and its roles in photoperiodic flowering of soybean GmCOL1 feed-forward loop and its roles in photoperiodic flowering of soybean. Front Plant Sci, 2019, 10:1221.
doi: 10.3389/fpls.2019.01221
[24] Zhao X H, Cao D, Huang Z J, Wang J L, Lu S J, Xu Y, Liu B H, Kong F J, Yuan X H. Dual functions of GmTOE4a in the regulation of photoperiod-mediated flowering and plant morphology in soybean. Plant Mol Biol, 2015, 88:343-355.
doi: 10.1007/s11103-015-0322-1
[1] ZHOU Qun, YUAN Rui, ZHU Kuan-Yu, WANG Zhi-Qin, YANG Jian-Chang. Characteristics of grain yield and nitrogen absorption and utilization of indica/japonica hybrid rice Yongyou 2640 under different nitrogen application rates [J]. Acta Agronomica Sinica, 2022, 48(9): 2285-2299.
[2] CHEN Zhi-Qing, FENG Yuan, WANG Rui, CUI Pei-Yuan, LU Hao, WEI Hai-Yan, ZHANG Hai-Peng, ZHANG Hong-Cheng. Effects of exogenous molybdenum on yield formation and nitrogen utilization in rice [J]. Acta Agronomica Sinica, 2022, 48(9): 2325-2338.
[3] WANG Yun-Qi, GAO Fu-Li, LI Ao, GUO Tong-Ji, QI Liu-Ran, ZENG Huan-Yu, ZHAO Jian-Yun, WANG Xiao-Ge, GAO Guo-Ying, YANG Jia-Peng, BAI Jin-Ze, MA Ya-Huan, LIANG Yue-Xin, ZHANG Rui. Variation of ear temperature after anthesis and its relationship with yield in wheat [J]. Acta Agronomica Sinica, 2022, 48(9): 2400-2408.
[4] LIU Cheng, ZHANG Ya-Xuan, CHEN Xian-Lian, HAN Wei, XING Guang-Nan, HE Jian-Bo, ZHANG Jiao-Ping, ZHANG Feng-Kai, SUN Lei, LI Ning, WANG Wu-Bin, GAI Jun-Yi. Wild segments associated with 100-seed weight and their candidate genes in a wild chromosome segment substitution line population [J]. Acta Agronomica Sinica, 2022, 48(8): 1884-1893.
[5] HUAI Yuan-Yuan, ZHANG Sheng-Rui, WU Ting-Ting, AZAM Muhammad, LI Jing, SUN Shi, HAN Tian-Fu, LI Bin, SUN Jun-Ming. Potential evaluation of molecular markers related to major nutritional quality traits in soybean breeding [J]. Acta Agronomica Sinica, 2022, 48(8): 1957-1976.
[6] LIU Kun, HUANG Jian, ZHOU Shen-Qi, ZHANG Wei-Yang, ZHANG Hao, GU Jun-Fei, LIU Li-Jun, YANG Jian-Chang. Effects of panicle nitrogen fertilizer rates on grain yield in super rice varieties with different panicle sizes and their mechanism [J]. Acta Agronomica Sinica, 2022, 48(8): 2028-2040.
[7] LI Xin, WANG Jian, LI Ya-Bing, HAN Ying-Chun, WANG Zhan-Biao, FENG Lu, WANG Guo-Ping, XIONG Shi-Wu, LI Cun-Dong, LI Xiao-Fei. Effects of different intercropping systems on cotton yield, biomass accumulation, and allocation [J]. Acta Agronomica Sinica, 2022, 48(8): 2041-2052.
[8] KE Dan-Xia, HUO Ya-Ya, LIU Yi, LI Jin-Ying, LIU Xiao-Xue. Functional analysis of GmTGA26 gene under salt stress in soybean [J]. Acta Agronomica Sinica, 2022, 48(7): 1697-1708.
[9] YANG Fei, ZHANG Zheng-Feng, NAN Bo, XIAO Ben-Ze. Genome-wide association analysis and candidate gene selection of yield related traits in rice [J]. Acta Agronomica Sinica, 2022, 48(7): 1813-1821.
[10] ZHANG Shao-Hua, DUAN Jian-Zhao, HE Li, JING Yu-Hang, Urs Christoph Schulthess, Azam Lashkari, GUO Tian-Cai, WANG Yong-Hua, FENG Wei. Wheat yield estimation from UAV platform based on multi-modal remote sensing data fusion [J]. Acta Agronomica Sinica, 2022, 48(7): 1746-1760.
[11] WANG Dan, ZHOU Bao-Yuan, MA Wei, GE Jun-Zhu, DING Zai-Song, LI Cong-Feng, ZHAO Ming. Characteristics of the annual distribution and utilization of climate resource for double maize cropping system in the middle reaches of Yangtze River [J]. Acta Agronomica Sinica, 2022, 48(6): 1437-1450.
[12] WANG Wang-Nian, GE Jun-Zhu, YANG Hai-Chang, YIN Fa-Ting, HUANG Tai-Li, KUAI Jie, WANG Jing, WANG Bo, ZHOU Guang-Sheng, FU Ting-Dong. Adaptation of feed crops to saline-alkali soil stress and effect of improving saline-alkali soil [J]. Acta Agronomica Sinica, 2022, 48(6): 1451-1462.
[13] YAN Jia-Qian, GU Yi-Biao, XUE Zhang-Yi, ZHOU Tian-Yang, GE Qian-Qian, ZHANG Hao, LIU Li-Jun, WANG Zhi-Qin, GU Jun-Fei, YANG Jian-Chang, ZHOU Zhen-Ling, XU Da-Yong. Different responses of rice cultivars to salt stress and the underlying mechanisms [J]. Acta Agronomica Sinica, 2022, 48(6): 1463-1475.
[14] YANG Huan, ZHOU Ying, CHEN Ping, DU Qing, ZHENG Ben-Chuan, PU Tian, WEN Jing, YANG Wen-Yu, YONG Tai-Wen. Effects of nutrient uptake and utilization on yield of maize-legume strip intercropping system [J]. Acta Agronomica Sinica, 2022, 48(6): 1476-1487.
[15] CHEN Jing, REN Bai-Zhao, ZHAO Bin, LIU Peng, ZHANG Ji-Wang. Regulation of leaf-spraying glycine betaine on yield formation and antioxidation of summer maize sowed in different dates [J]. Acta Agronomica Sinica, 2022, 48(6): 1502-1515.
Full text



[1] WANG Li-Yan;ZHAO Ke-Fu. Some Physiological Response of Zea mays under Salt-stress[J]. Acta Agron Sin, 2005, 31(02): 264 -268 .
[2] Qi Zhixiang;Yang Youming;Zhang Cunhua;Xu Chunian;Zhai Zhixi. Cloning and Analysis of cDNA Related to the Genes of Secondary Wall Thickening of Cotton (Gossypium hirsutum L.) Fiber[J]. Acta Agron Sin, 2003, 29(06): 860 -866 .
[3] NI Da-Hu;YI Cheng-Xin;LI Li;WANG Xiu-Feng;ZHANG Yi;ZHAO Kai-Jun;WANG Chun-Lian;ZHANG Qi;WANG Wen-Xiang;YANG Jian-Bo. Developing Rice Lines Resistant to Bacterial Blight and Blast with Molecular Marker-Assisted Selection[J]. Acta Agron Sin, 2008, 34(01): 100 -105 .
[4] DAI Xiao-Jun;LIANG Man-Zhong;CHEN Liang-Bi. Comparison of rDNA Internal Transcribed Spacer Sequences in Oryza sativa L.[J]. Acta Agron Sin, 2007, 33(11): 1874 -1878 .
[5] WANG Bao-Hua;WU Yao-Ting;HUANG Nai-Tai;GUO Wang-Zhen;ZHU Xie-Fei;ZHANG Tian-Zhen. QTL Analysis of Epistatic Effects on Yield and Yield Component Traits for Elite Hybrid Derived-RILs in Upland Cotton[J]. Acta Agron Sin, 2007, 33(11): 1755 -1762 .
[6] WANG Chun-Mei;FENG Yi-Gao;ZHUANG Li-Fang;CAO Ya-Ping;QI Zeng-Jun;BIE Tong-De;CAO Ai-Zhong;CHEN Pei-Du. Screening of Chromosome-Specific Markers for Chromosome 1R of Secale cereale, 1V of Haynaldia villosa and 1Rk#1 of Roegneria kamoji[J]. Acta Agron Sin, 2007, 33(11): 1741 -1747 .
[7] Zhao Qinghua;Huang Jianhua;Yan Changjing. A STUDY ON THE POLLEN GERMINATION OF BRASSICA NAPUS L.[J]. Acta Agron Sin, 1986, (01): 15 -20 .
[8] ZHOU Lu-Ying;LI Xiang-Dong;WANG Li-Li;TANG Xiao;LIN Ying-Jie. Effects of Different Ca Applications on Physiological Characteristics, Yield and Quality in Peanut[J]. Acta Agron Sin, 2008, 34(05): 879 -885 .
[9] WANG Li-Xin; LI Yun-Fu; CHANG Li-Fang; HUANG Lan ;; LI Hong-Bo ; GE Ling-Ling; Liu Li-Hua ;; YAO Ji ;; ZHAO Chang-Ping ;. Method of ID Constitution for Wheat Cultivars[J]. Acta Agron Sin, 2007, 33(10): 1738 -1740 .
[10] ZHENG Tian-Qing;XU Jian-Long;FU Bing-Ying;GAO Yong-Ming;Satish VERUKA;Renee LAFITTE;ZHAI Hu-Qu;WAN Jian-Min;ZHU Ling-Hua;LI Zhi-Kang. Preliminary Identification of Genetic Overlaps between Sheath Blight Resistance and Drought Tolerance in the Introgression Lines from Directional Selection[J]. Acta Agron Sin, 2007, 33(08): 1380 -1384 .