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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (8): 2097-2104.doi: 10.3724/SP.J.1006.2023.24184

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

Identification of major QTLs for nodule formation in peanut

HUANG Li, CHEN Wei-Gang, LI Wei-Tao, YU Bo-Lun, GUO Jian-Bin, ZHOU Xiao-Jing, LUO Huai-Yong, LIU Nian, 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:2022-08-09 Accepted:2023-02-10 Online:2023-08-12 Published:2023-02-22
  • Contact: JIANG Hui-Fang E-mail:peanutlab@oilcrops.cn
  • Supported by:
    China Agriculture Research System of MOF and MARA(CARS-13);Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(2022-2060299-089-031)

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Abstract:

Peanut is an important oil and economic crop of legumes in China. Nodules are important for symbiotic nitrogen fixation in peanut. Dissecting the genetic basis of nodule formation could promote the understanding of nitrogen fixation ability and characteristics of nodules in peanut. However, there are few studies on nodule formation and the genetic basis of nodule formation remained unclear in peanut. In this study, the nodules were investigated in a high generation RIL population and seven lines were identified without nodule. The chlorophyll content, plant height, fresh weight per plant, and dry weight per plant of the lines without nodule were significantly lower than those of parents. Using the previous genetic linkage map based on SSR markers, major QTLs qPNA08 and qPNB07 were identified on chromosome A08 and B07, respectively. The InDel markers in the two major QTLs were developed by the genome resequencing data of parents and performed amplification in the RILs. The interval of QTLs qPNA08 and qPNB07 was reduced to 1.6 Mb and 1.8 Mb, respectively. Meanwhile, the phenotypic variation explained of these two QTLs was increased to 16.4% and 9.9%, respectively. There were four and two nodulin genes variation loci in the two target intervals, respectively. This study provided the understanding for unveiling the genetic basis of formation and development of nodule and symbiotic nitrogen fixation in peanut.

Key words: peanut, nodule formation, QTLs mapping, linkage analysis

Fig. 1

Peanut plants with root and nodules A: root with nodules; B: root without nodules."

Table 1

Evaluation of chlorophyll content and agronomic traits of lines without nodules and parental lines"

材料
Accession		 叶绿素
Chlorophyll content (SPAD)		 株高
Plant height
(cm)		 单株植株鲜重
Fresh weight per plant
(g)		 单株荚果干重
Dry weight per plant
(g)
2019 2020 2019 2020 2019 2020 2019 2020
L039 28.81 29.07 30.33 28.23 168.3 129.0 24.2 27.4
L053 26.34 27.54 32.33 33.75 126.3 126.9 21.6 27.4
L086 26.27 24.43 32.70 36.46 157.5 139.0 20.9 24.8
L097 27.37 28.38 35.13 38.75 160.0 208.8 24.4 21.0
L099 25.03 24.37 51.89 52.44 187.0 218.0 25.7 29.6
L135 29.22 29.97 37.12 39.63 139.0 145.0 20.2 20.1
L140 20.41 25.14 38.52 39.12 202.5 119.0 16.1 19.5
中花10号Zhonghua 10 43.91 45.80 47.25 50.90 493.3 322.5 56.6 58.1
ICG12625 40.92 46.18 66.56 61.24 530.3 411.0 32.8 37.3

Table 2

Identification of major QTL for nodule formation in peanut RILs"

位点
QTL		 连锁群
Linkage group		 阈值
LOD		 遗传变异解释率
PVE (%)		 加性效应
Additive effect		 标记区间
Marker internal		 物理位置
Physical position (Mb)
qPNA08 A08 3.7 9.1 0.067 AHGS1880-AGGS1495 9.5-14.2
qPNB07 B07 3.1 7.1 -0.061 Ai07B24086-Ai07B26973 118.7-128.6

Table 3

Information of major QTLs for nodules formation in peanut RILs"

位点
QTL		 连锁群
Linkage group		 阈值
LOD		 遗传变异解释率
PVE (%)		 加性效应
Additive effect		 标记区间
Marker internal		 物理位置
Physical position (Mb)
qPNA08 A08 5.9 16.4 0.100 InDelA08-3-InDelA08-6 10.8-12.4
qPNB07 B07 3.7 9.9 -0.074 InDelB07-13-InDelB07-17 126.4-128.1

Fig. 2

Major QTLs for nodules formation in peanut"

Table 4

Annotation of SNP and InDel in the major QTLs for nodules formation"

类别
Category		 qPNA08 qPNB07
数量
Number		 比例
Ratio (%)		 数量
Number		 比例
Ratio (%)
基因间区Intergenic region 183 77.22 226 84.01
上游/下游区Upstream/downstream region 20 8.44 23 8.55
上游区Upstream region 11 4.64 15 5.58
下游区Downstream region 6 2.53 8 2.97
上游区&下游区Upstream & downstream region 3 1.27 0 0
基因区Genic region 34 14.35 20 7.43
内含子Intronic 18 7.59 14 5.20
外显子Exonic 8 3.38 3 1.12
同义突变Synonymous 3 1.27 0 0
非同义突变Nonsynonymous 5 2.11 1 0.37
终止突变Stopgain 0 0 1 0.37
非移码缺失Nonframeshift deletion 0 0 1 0.37
5′UTR区5′UTR 4 1.69 2 0.74
3′UTR区3′UTR 3 1.27 1 0.37
剪切区Splicing region 1 0.42 0 0

Table 5

Information of nodulin genes with variation locus between parents in the gene region"

基因
Gene ID		 染色体
Chromosome		 位置
Position		 中花10号基因型
Genotype in
Zhonghua 10		 ICG12625基因型
Genotype in ICG12625		 变异位置
Variation
location
arahy 0GM2Z0 A08 11170576 GA G 上游区Upstream
arahy 9F81FQ A08 11024163 A G 上游区Upstream
A08 11024537 C T 上游区Upstream
A08 11020291 CAT C 3′UTR区3′UTR
arahy L4R73E A08 11107037 G C 剪切区Splicing
arahy M7858J A08 11066800 A ATAT 上游区Upstream
arahy AT5BZQ B07 126823960 T C 上游区Upstream
B07 126822807 CCT C 5′UTR区5′UTR
arahy DE00KI B07 127083363 A G 上游区Upstream

Table 6

Expression of nodulin genes in the major QTL regions in the root and nodule"

基因
Gene ID		 染色体
Chromosome		 基因位置
Position (bp)		 根
Root		 根瘤
Nodule
arahy.9F81FQ A08 11020073-11024051 123.72 8.76
arahy.L4R73E A08 11104688-11110744 54.76 4.52
arahy.M7858J A08 11061653-11066507 9.91 71.95
arahy.0GM2Z0 A08 11168701-11170133 0.14 8.91
arahy.AT5BZQ B07 127473205-127478066 99.18 18.578
arahy.QHG6EX B07 127589943-127595947 31.83 0.57
arahy.I1VTPH B07 127508511-127513030 2.99 19.23
arahy.DE00KI B07 127733203-127737565 0.59 10.17
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