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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (8): 1894-1904.doi: 10.3724/SP.J.1006.2022.14114

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

QTLs analysis for reticulation thickness based on reconstruction of three dimensional models in peanut pods

ZHANG Sheng-Zhong1(), HU Xiao-Hui1, CI Dun-Wei1, YANG Wei-Qiang1, WANG Fei-Fei1, QIU Jun-Lan2, ZHANG Tian-Yu3, ZHONG Wen3, YU Hao-Liang4, SUN Dong-Ping4, SHAO Zhan-Gong5, MIAO Hua-Rong1,*(), CHEN Jing1,*()   

  1. 1Shandong Peanut Research Institute, Qingdao 266100, Shandong, China
    2Weihai Seed Management Station, Weihai 264200, Shandong, China
    3Shandong Seed Administration Station, Jinan 250100, Shandong, China
    4Yantai Fenglin Foodstuff Co., Ltd, Yantai 264108, Shandong, China
    5Agricultural and Rural Bureau of Laixi City, Qingdao 266600, Shandong, China
  • Received:2021-07-01 Accepted:2021-11-29 Online:2022-08-12 Published:2021-12-28
  • Contact: MIAO Hua-Rong,CHEN Jing E-mail:593318769@qq.com;1949813628@qq.com;mianbaohua2008@126.com
  • Supported by:
    National Natural Science Foundation of China(32001584);Breeding Project from Department Science & Technology of Shandong Province(2020LZGC001);Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences(CXGC2021A09);Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences(CXGC2021A46);Qingdao People's Livelihood Science and Technology Program(20-3-4-26-nsh)

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Abstract:

The thickness of pod reticulation is not only an important criterion of peanut taxonomy, but also an agronomy trait related to peanut mechanical harvesting. To explore the genetic mechanism of reticulation thickness of peanut pods, a novel phenotyping method was developed to determine the reticulation thickness through reconstructing three dimensional (3D) models of pods. Meanwhile, a recombinant inbred line (RIL) population (181 lines) was derived from a cross between Huayu 36 and 6-13 and planted in three environments from 2019 to 2020, including Qingdao, Dongying, and Weihai of Shandong province. Phenotypic data of the RIL population were collected from these three environments. Two related traits, thicknesses of latitudinal and longitudinal protuberant veins (reticulations), had continuous and transgressive distributions in the RIL population, with broad-sense heritablities of 0.92 and 0.91, respectively. Based on a previous high density genetic map, a total of 11 additive QTLs were identified explaining phenotypic variations of 5.21%-11.06%, among which six QTLs were related to thickness of latitudinal protuberant vein and five related to thickness of longitudinal protuberant vein. Two major loci, qLA2 and qLO9 could be detected in more than one environments, with contributing alleles coming from Huayu 36 and 6-13, respectively. A total of 22 pairs of epistatic QTLs involving 34 loci were identified explaining phenotypic variations of 0.55%-4.37%, among which 10 pairs of interactions were related to thickness of latitudinal protuberant vein and 12 pairs were related to thickness of longitudinal protuberant vein. These results provide valuable information for further gene mapping and molecular breeding in peanut.

Key words: peanut, pod reticulation, QTLs, additive, epistatic

Fig. 1

Workflow for evaluation of pod reticulation through 3D model reconstruction in peanut A: the multiple positions for camera shooting; B: the obtained pod image sequences; C: key point matching; D: construction of sparse point cloud; E: construction of dense point cloud; F: reconstruction of the mesh surface of 3D model; G: collection of 3D coordinates of specific points. The white rectangle represents the target area for pod reticulation evaluation. The red-green-blue symbol represents a 3D image."

Fig. 2

Comparison of two measurement strategies for pod reticulation thickness A: the image of 7 peanut cultivars (or lines); B: the 3D models of 7 peanut cultivars (or lines) and the red-green-blue symbol representing 3D image; C: thickness measurement of pod reticulation based on reticulation removing stratedgy; D: thickness measurement of pod reticulation based on 3D model reconstruction strategy. Different lowercase letters (a, b, c, and d) represent significant difference at P = 0.05 level by multiple comparison (LSD). The red-green-blue symbol represents a 3D image."

Fig. 3

Phenotypic variation of pod reticulation thickness among two parents and certain RILs The red-green-blue symbol represents a 3D image."

Table 1

Statistics analysis of phenotypic data for two parents and its RIL population"

性状
Trait		 环境Environment 亲本Parents RIL群体RIL population
花育36号Huayu 36 6-13 平均值Mean 标准差SD 最小值Min. 最大值Max. 峰度Kurt. 偏度Skew. Shapiro-Wilk
横纹厚度
LA (mm)		 E1 0.2431 0.0293** 0.1902 0.0829 0.0167 0.4448 -0.12 0.10 0.989*
E2 0.2320 0.0514** 0.1731 0.0914 0.0147 0.4854 0.54 0.60 0.977**
E3 0.1961 0.0496** 0.1993 0.0909 0.0101 0.4854 0.26 0.31 0.986*
纵纹厚度
LO (mm)		 E1 0.4003 0.7165** 0.4884 0.1138 0.2704 0.7673 -0.27 0.50 0.970
E2 0.3811 0.7356** 0.4871 0.1277 0.2538 0.9096 -0.11 0.37 0.981**
E3 0.4278 0.7490** 0.4777 0.1340 0.1788 0.8519 0.74 0.81 0.948

Fig. 4

Frequency distribution of pod reticulation in RIL population across different environments"

Table 2

Variance analysis of the pod reticulation related traits"

性状Trait 来源Source 自由度DF 方差SS 标准差MS F值F-value P值P value 遗传率h2
横纹厚度
LA		 基因型G 169 0.0851 0.0005 20.4911 P<0.001 0.92
环境E 2 0.0015 0.0007 29.6624 P<0.001
基因型×环境G × E 252 0.0148 0.0001 2.3888 P<0.001
误差Error 833 0.0205 0
纵纹厚度
LO		 基因型G 169 0.1643 0.0010 13.9010 P<0.001 0.91
环境E 2 0.0003 0.0002 2.2961 P<0.001
基因型×环境G × E 252 0.0311 0.0001 1.7620 P<0.001
误差Error 832 0.0582 0.0001

Fig. 5

QTL location on linkage groups in different environments Red and blue colors represent the thicknesses of latitudinal and longitudinal protuberant veins, respectively."

Table 3

Information of QTLs related to peanut pod reticulation"

性状
Trait		 QTL 环境Env. 染色体Chr. 标记区间
Marker interval		 置信区间
C.I. (cM)		 LOD 加性效应Add 贡献率PVE (%)
横纹厚度
LA		 qLA2 E1 2 Marker938-Marker875 0-3.9 3.31 -0.0030 11.06
E2 2 Marker938-Marker875 0-5.6 2.91 -0.0029 6.08
E3 2 Marker938-Marker864 0-2.8 3.70 -0.0039 7.44
qLA3 E1 3 Marker1868-Marker1876 24.8-34.2 2.93 0.0028 5.62
qLA12 E3 12 Marker6681-Marker6697 91-105.2 2.64 0.0021 5.21
qLA15 E1 15 Marker9048-Marker9075 35-53.1 2.83 -0.0034 5.34
qLA16.1 E1 16 Marker9463-Marker10015 0.9-11.2 4.30 0.0047 10.79
qLA16.2 E2 16 Marker10139-Marker10315 19.3-24.8 3.59 -0.0034 7.55
纵纹厚度
LO		 qLO4 E1 4 Marker2874-3754F 35-53.1 3.21 -0.0034 8.31
E3 4 Marker2874-3754F 34.3-52.7 3.10 -0.0040 8.74
qLO9 E1 9 Marker4980-Marker5581 0.9-11.2 3.76 0.0047 10.96
E2 9 Marker4980-Marker5533 1-11.2 3.85 0.0050 10.99
qLO12 E3 12 Marker6697-Marker6722 96-105.5 4.07 0.0045 10.71
qLO17 E2 17 Marker10418-Marker10431 0-8.4 2.61 -0.0033 6.05
qLO19 E2 19 Marker11749-Marker11769 11.5-15.5 3.10 0.0047 7.26

Table 4

Information of epistatic QTLs related to peanut pod reticulation"

性状
Trait		 QTLi 染色体Chr. 标记区间
Marker interval		 QTLj 染色体Chr. 标记区间
Marker interval		 LOD 上位性效应
AA		 贡献率
PVE (%)
横纹厚度
LA		 Epi-qLA1 1 Marker344-Marker340 Epi-qLA7 7 AHGS0035-AHGS1954 5.57 0.0015 2.72
Epi-qLA2 2 Marker862-Marker746 Epi-qLA3.1 3 Marker1177-Marker1191 5.73 0.0021 2.64
Epi-qLA3.2 3 Marker1894-Marker1906 Epi-qLA10.3 10 Marker5972-Marker5996 5.24 0.0016 2.58
Epi-qLA3.2 3 Marker1894-Marker1906 Epi-qLA12 12 Marker6650-Marker6653 5.03 0.0017 2.82
Epi-qLA3.2 3 Marker1894-Marker1906 Epi-qLA16 16 Marker10343-Marker10344 5.44 0.0021 2.77
Epi-qLA5.1 5 Marker3174-Marker3169 Epi-qLA5.2 5 Marker3064-Marker3055 5.32 0.0023 1.77
Epi-qLA5.2 5 Marker3064-Marker3055 Epi-qLA10.2 10 Marker5872-Marker5972 6.93 0.0027 3.50
Epi-qLA5.1 5 Marker3174-Marker3169 Epi-qLA19 19 AHGS1634-Marker11752 5.26 -0.0015 2.65
Epi-qLA8 8 Marker4781-Marker4778 Epi-qLA9 9 Marker5648-Marker5656 5.93 0.0016 3.17
Epi-qLA9 9 Marker5648-Marker5656 Epi-qLA10.1 10 Marker5953-Marker5941 5.90 -0.0016 3.15
纵纹厚度
LO		 Epi-qLO1.1 1 Marker25-Marker11 Epi-qLO15 15 Marker8480-Marker8432 5.44 0.1933 2.40
Epi-qLO1.2 1 Marker597-Marker601 Epi-qLO11.2 11 Marker6349-Marker6352 5.55 0.0957 3.69
Epi-qLO3 3 Marker1177-Marker1191 Epi-qLO11.1 11 Marker6220-Marker6275 9.91 -0.1251 4.37
Epi-qLO5 5 Marker3174-Marker3169 Epi-qLO10.2 10 Marker5872-Marker5972 5.46 -0.1136 3.51
Epi-qLO6.1 6 Marker3659-Marker3660 Epi-qLO20 20 Marker12781-Marker12791 6.64 0.1012 0.55
Epi-qLO6.2 6 Marker4191-Marker4236 Epi-qLO8.1 8 Marker4862-Marker4875 6.99 -0.1060 3.32
Epi-qLO7 7 Marker4658-Marker4605 Epi-qLO18 18 Marker11664-Marker11669 5.06 -0.1120 3.76
Epi-qLO8.2 8 AGGS1495-Marker4770 Epi-qLO15.2 15 Marker8513-Marker8628 6.83 -0.1403 1.91
Epi-qLO10.1 10 Marker5877-Marker5872 Epi-qLO11.1 11 Marker6220-Marker6275 5.39 0.2010 1.57
Epi-qLO10.2 10 Marker5872-Marker5972 Epi-qLO15.2 15 Marker8513-Marker8628 6.75 0.2029 3.89
Epi-qLO10.2 10 Marker5872-Marker5972 Epi-qLO16 17 Marker10786-C123 5.04 0.1245 2.59
Epi-qLO13 13 Marker6815-Marker6823 Epi-qLO15.1 15 Marker8503-Marker8489 5.52 0.1190 3.37
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