Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (13): 2208-2219.doi: 10.3864/j.issn.0578-1752.2019.13.002

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

QTL Mapping of Hard Seededness in Wild Soybean Using BSA Method

CHEN JingJing,LIU XieXiang,YU LiLi,LU YiPeng,ZHANG SiTian,ZHANG HaoChen,GUAN RongXia(),QIU LiJuan   

  1. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Germplasm Utilization, Ministry of Agriculture, Beijing 100081
  • Received:2019-02-28 Accepted:2019-04-14 Online:2019-07-01 Published:2019-07-11
  • Contact: RongXia GUAN E-mail:guanrongxia@caas.cn

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Abstract:

【Objective】 Hard seededness of wild soybean is an important effector that limits the utilization of wild resources in soybean genetic improvement. Bulked segregant analysis (BSA) was employed to identify major quantitative trait loci (QTLs) related with hard seededness in soybean, which laid a foundation for effective utilization of wild soybean germplasm in cultivated soybean improvement. 【Method】 F2 and F7 segregation populations were constructed from a cross between cultivated soybean Zhonghuang39 and wild soybean NY27-38. Uniformly sized seeds were selected from each line, and 30 seeds were soaked in a petri dish with 30 mL distilled water for 4 hours at 25℃. The assay was replicated 3 times. The number of permeable and impermeable seeds were counted. In F2 population, the first DNA pool was constructed from 22 individuals with permeable seeds (imbibition rate ＞90%), and second DNA pool was constructed from 16 individuals with impermeable seeds (imbibition rate ＜10%). In F7 population, 20 lines with permeable seeds (100% imbibition) and 20 lines with impermeable seeds (no imbibition) were used to construct two DNA pools, respectively. To detect genomic regions associated with hard seededness, these DNA bulks were genotyped with 259 polymorphic SSR markers to identify markers linked to QTL. A linkage map was constructed with 192 SSR markers, QTLs related with hard seededness were identified by composite interval mapping in F7 segregation population. 【Result】 Out of 259 SSR loci polymorphic between Zhonghuang39 and NY27-38, 10 and eight polymorphic SSR markers between the permeable and impermeable pools were detected in 16.3 Mb interval on chromosome 2 and 23.4 Mb interval on chromosome 6, respectively, in F2 population. The QTL region (276.0 kb) located between Satt274 and Sat_198 on chromosome 2 contained previously cloned gene GmHs1-1, the QTL explained 17.2% of the total genetic variation. The other QTL was mapped on chromosome 6 flanked by BARCSOYSSR_06_0993 and BARCSOYSSR_06_1068, accounting for 17.8% of the total genetic variation. In F7 population, eleven, nine and four SSR polymorphic markers between the permeable and impermeable pools were detected in 27.4 Mb interval on chromosome 2, 27.8 Mb interval on chromosome 6, 18.2 Mb interval on chromosome 3, respectively. A linkage map of 192 SSR markers and covering 2 390.2 cM was constructed through composite interval mapping in F7 population. Three QTLs related with hard seededness were detected. The QTL on chromosome 2 located between Satt274 and Sat_198, explained 23.3% of the total genetic variation; the QTL on chromosome 6 flanked by Sat_402 and Satt557, explained 20.4% of the total genetic variation; the QTL on chromosome 3 flanked by Sat_266 and Sat_236 accounted for 4.9% of the total genetic variation. 【Conclusion】 In this study, three QTLs related to soybean hard seededness were identified by both BSA and traditional linkage mapping, indicating that BSA is an effective strategy for identifying QTLs in soybean.

Key words: soybean, hard seededness, QTL mapping

Fig. 1

Hard seededness of Zhonghuang39, NY27-38, F1:2 seeds and F2, F7 populations A: Phenotypic illustration of Zhonghuang39, NY27-38 and F1:2 seeds from a F1 plant (Zhonghong39 × NY27-38) at 0, 2 and 4 h; B: Permeable proportion of seeds from Zhonghuang39, NY27-38 and their F1:2 progeny at multiple time points over 12 h; C: Frequency distribution for seed-coat permeability of F2 population; D: Frequency distribution for seed-coat permeability of F7 population"

Fig. 2

Phenotypic distribution for seed-coat permeability with different seed coat colors of F2 and F7 populations A: Photographic illustration of seed-coat permeability with different seed-coat colors of F2 population at 4 h; B: Relationship of seed-coat colors and frequency distribution of permeability in F2 population; C: Relationship of seed-coat colors and frequency distribution of permeability in F7 population"

Fig. 3

Identification of polymorphic SSR markers between two DNA bulks of F2 population Polymorphic SSR markers between two DNA bulks on chromosome 2 (A) and chromosome 6 (B). 1: Permeable DNA bulk; 2: Impermeable DNA bulk"

Fig. 4

Identification of polymorphic SSR markers between two DNA bulks of F7 population Polymorphic SSR markers between two DNA bulks on chromosome 2 (A), chromosome 6 (B) and chromosome 3 (C). 1: Permeable DNA bulk; 2: Impermeable DNA bulk"

Table 1

QTLs for hard seededness of soybean in different populations"

群体
Population		 染色体
Chr.		 标记区间
Marker interval		 区间物理位置
Physical position of interval (bp,Wm82.a1.v1.1)		 LOD值
LOD value		 贡献率
PVE (%)		 加性效应
Additive effect
F2 2 Satt274-Sat_198 48345948—48621931 13.3 17.2 15.8
6 6-0993-6-1068 18697727—20742109 13.0 17.8 12.5
F7 2 Satt274-Sat_198 48345948—48621931 14.0 23.3 20.2
3 Sat_266-Sat_236 36046708—37622037 2.7 4.9 8.9
6 Sat_402-Satt557 16367687—20018845 11.5 20.4 19.2

Fig. 5

Violin plots showing the effect of different alleles of QTLs on seed permeability A: F2 population; B: F7 population"

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