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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (5): 1222-1230.doi: 10.3724/SP.J.1006.2023.24140

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

Development and employment of InDel marker in peanut QTL mapping of oil content

TAO Shun-Yu(), WU Bei, LIU Nian, LUO Huai-Yong, HUANG Li, ZHOU Xiao-Jing, CHEN Wei-Gang, GUO Jian-Bin, YU Bo-Lun, LEI Yong, LIAO Bo-Shou, JIANG Hui-Fang()   

  1. Oil Crops Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, Hubei, China
  • Received:2022-06-10 Accepted:2022-07-21 Online:2023-05-12 Published:2022-09-23
  • Contact: *E-mail: peanutlab@oilcrops.cn
  • Supported by:
    Key Area Research and Development Program of Guangdong Province(2020B020219003);National Natural Science Foundation of China(31801403);National Natural Science Foundation of China(31871666);Crop Germplasm Resources Protection Project(2017NWB033);Plant Germplasm Resources Sharing Platform(NICGR2017-36);China Agriculture Research System of MOF and MARA(CARS13);Innovation Project of Chinese Academy of Agricultural Sciences(2022-2060299-089-031)

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Abstract:

The developing of stable and efficient molecular markers is of great value for marker-assisted selection of peanut varieties with high oil content. In this study, two parents with significant differences in oil content, Xuhua 13 (high oil content) and Zhonghua 6 (low oil content), were used to detect genomic structural variation by PacBio third-generation sequencing technology, and 35,794 and 74,703 structural variations were detected in Xuhua 13 and Zhonghua 6, respectively. 84 InDel markers in the target region were detected based on the parents’ structural variations and the previous QTL mapping information. And 9 InDel markers were found to be polymorphic between the parents. Meanwhile, F2 population with 1160 individual plants was constructed based on near isogenic lines (NILs) derived from heterozygous residuals in the recombined inbred line (RIL) population. The polymorphic markers were used to genotype the population and to construct the genetic linkage map with 149.84 cM. Combining with phenotype data of population for oil content, QTL (qOCA08) was fine mapped between marker M23 and marker M11, which was located on 1.2 Mb interval of chromosome A08. This study demonstrated the feasibility of InDel marker for peanut QTL mapping. The locus of oil content and closely linked InDel markers can provide the theoretical and technical guidance for peanut molecular marker-assisted breeding.

Key words: peanut, genome resequencing, InDel, oil content

Table 1

Sequencing information of parents"

样品
Sample name		 碱基数目
Base number		 Reads数
Clean reads		 比对率
Mapping rate (%)		 覆盖度
Coverage
(%)		 结构变异
Structural variation		 插入
Insertion		 缺失
Deletion
徐花13 Xuhua 13 81,826,464,736 5,615,798 98.03 96.91 35,794 12,293 4496
中花6号 Zhonghua 6 68,494,830,848 4,225,186 97.58 96.59 74,703 26,833 12,906

Fig. 1

Length distribution of insertion and deletion variations in two parents A: length distribution of insertion variation in Xuhua 13; B: length distribution of deletion variation in Xuhua 13; C: length distribution of insertion variation in Zhonghua 6; D: length distribution of deletion variation in Zhonghua 6."

Fig. 2

Ratio of different genomic region with structural variations A: the ratio of different genomic region with structural variations in Xuhua 13; B: the ratio of different genomic region with structural variations in Zhonghua 6."

Fig. 3

Polymorphic PCR amplication of nine InDel markers between two parents M1: 2000 bp; M2: 5000 bp. M9: InDel-A08-37791529; M21: InDel-A08-42578036; M6: InDel-A08-44213248; M22: InDel-A08-44339712; M23: InDel-A08-44988232; M11: InDel-A08-46212241; M13: InDel-A08-46400655; M14: InDel-A08-46555343; M8: InDel-A08- 49660135."

Table 2

Information of InDel marker primer"

引物名称
Primer name		 引物序列
Primer sequences (5'-3')		 引物位置(A08)
Physical position (A08) (bp)		 差异大小
Difference in size (bp)
M9-F AGTATTGAAGCGGCAGGAGG 37,791,529 18
M9-R TTGCACTTCGATGTGGAGGAT
M21-F TAGTTCTCTCCGGATGCCTCA 42,578,036 26
M21-R TGCCATGAAATTACTCATTACTCTT
M6-F CAGAGAGACAGAGAGCGAGC 44,213,248 466
M6-R TGAGCCGGATGAGTAAGACA
M22-F AATAAGTTTGTTGGGAGAATGAAAT 44,339,712 24
M22-R GCTCCCATTGTCTAGCGAAAAC
M23-F TGCTGTGTGTAATAGTTAGAGGCT 44,988,232 28
M23-R TGGGGTGAGTGAATTATACGTGA
M11-F TGTGAGTACCGACATACACTCA 46,212,241 154
M11-R AATTTGATTATTGGACATCCCCT
M13-F GTTGAGACCGGAACACAGGA 46,400,655 362
M13-R CTATCCACTAGGTTCTCCAGCA
M14-F TGTCAATGTGTTATCATCTCAATTT 46,555,343 2353
M14-R TAATTGGCACCACGCAATGTC
M8-F CCAAGTCCTTTGCAGCTCTC 49,660,135 15
M8-R AAATTACTTTCAGTAAATGTCTAGC

Fig. 4

Frequency distribution of oil content in F2 population"

Fig. 5

QTL mapping for oil content in F2 population"

Fig. 6

Genotypic effects of oil content of alleles at M11 locus ** represents significant difference at the 0.01 probability level by t-test."

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