Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (23): 4761-4773.doi: 10.3864/j.issn.0578-1752.2024.23.014

• HORTICULTURE • Previous Articles     Next Articles

Genetic Diversity Analysis of Mandarin and Excellent Germplasm Screening Based on Whole-Genome Resequencing Data and Phenotypic Traits

LI Pei1(), HE ZhiLin1, TAN YueXia1, ZHAO WanTong1, FENG JinYing1, CHEN GuiHu2, YAN Chi2, WANG ZiHao2, HUANG Ping2, JIANG Dong1()   

  1. 1 Citrus Research Institute, Southwest University, Chongqing 400712
    2 King of Fruit Horticultural Research Institute, Chongqing 400712
  • Received:2024-04-08 Accepted:2024-05-15 Online:2024-12-01 Published:2024-12-07

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Abstract:

【Objective】 In this study, the whole-genome resequencing data and phenotypic identification information were used to reveal the genetic variation and population structure of mandarin germplasm resources and to explore elite citrus germplasms with these information, the aim was to promote citrus variety improvement in the direction of high fruit quality and diversification. 【Method】 In 2021 and 2022, 25 phenotypic traits of fruits and flowers of 473 mandarin accessions were identified in two consecutive years, and the young leaves were collected for DNA extraction, library construction and sequencing. Diversity analysis of phenotypic information was carried out using the variation coefficient and Shannon-Wiener index. To screen out excellent mandarin germplasm, a comprehensive evaluation on mandarin germplasm resources was conducted using correlation analysis, cluster analysis, and principal component analysis. Phylogenetic tree analysis was performed based on resequencing data to analyze the characteristics of the group to which the excellent germplasm belongs. 【Result】 There are extensive variations and rich genetic diversity in 473 mandarin accessions. The variation coefficient of 21 quantitative traits ranges from 9.36% to 76.98%, with an average of 34.95%. and the genetic diversity index from 1.71 to 2.08, with an average of 1.93. The diversity index of the four qualitative traits ranged from 0.35 to 0.98, which was significantly lower than the quantitative traits. Among them, the variation coefficient of segment membrane and juice sac wall weight is the largest, and peel color have the largest genetic diversity index. Principal component analysis was performed on 17 fruit phenotypes, and the top five principal components have the cumulative contribution rate more than 70%. Factor analysis was used to conduct a comprehensive evaluation, it was used to select elite mandarin accessions with the comprehensive evaluation score which ranged from -1.23 to 1.59, the cultivar with the highest score was LP31 (Nishinokaori×Jin Kui), followed by LP45 (Nishinokaori×Jin Kui), LP18 (Benimadona×American Tang Ju), LP3 (Tarocco Blood Orange×Jin Kui). Both the phenotypic cluster analysis results and the phylogenetic tree analysis divided the tested mandarin germplasm resources into 7 groups, different groups can reflect the differences in the origin, variety type and hybrid combination derived from different genetic backgrounds. The germplasms with high comprehensive evaluation scores mostly are concentrated in Group Ⅳ, which showed that these excellent germplasms have similar genetic component. 【Conclusion】 The 473 mandarin accessions used in this study has extensive phenotypic variation and rich genetic diversity. The phenotypic cluster analysis results and phylogenetic tree gave similar classification results, and the excellent germplasm selected based on comprehensive evaluation score have high genetic similarity.

Key words: mandarin, phenotypic identification, genetic diversity, whole-genome resequencing, phylogenetic evolution

Table 1

Described grouping for quality traits of mandarin germplasm resource"

性状
Traits		 分组Group
1 2 3
单/多胚 Mono- or poly-embryony 单胚 Monoembryony 多胚 Polyembryony
花药颜色 Anthers color 白色 White 淡黄色 Pale yellow 黄色 Yellow
柱头位置 Stigma position 柱头低于花药 Low 柱头与花药平齐 Middle 柱头高于花药 High
柱头形态 Stigma pattern 直立 Straight 弯曲 Bend

Table 2

Distribution frequency and diversity index of quality traits of mandarin"

性状
Traits		 分布频率The distributions of frequency (%) 多样性指数
H
1 2 3
单多胚 Mono- or poly-embryony 61 39 0.67
花药颜色 Anthers color 2 14 84 0.50
柱头位置 Stigma position 44 12 44 0.98
柱头形态 Stigma pattern 91 9 0.37

Table 3

Description of quantitative traits and diversity index of mandarin germplasm resources"

性状
Traits		 最小值
Min		 最大值
Max		 均值±标准差
Mean±SD		 中位数
Med		 变异系数
CV (%)		 多样性指数
H
单果重FW (g) 16.06 442.51 102.84±58.93 87.02 57.30 1.88
果实横径FD (cm) 3.13 9.72 5.70±1.17 5.55 20.55 2.05
果实纵径FL (cm) 2.02 9.21 4.61±1.04 4.47 22.51 2.03
果形指数FSI 0.56 1.09 0.81±0.09 0.80 10.67 2.05
果皮厚度PT (cm) 0.10 0.56 0.28±0.08 0.30 28.76 1.87
单果皮重PW (g) 4.06 135.68 28.11±18.12 23.63 64.48 1.79
囊瓣数SNPF 6.70 13.70 9.72±1.10 9.70 11.34 2.06
单果种粒数SNF 0.00 37.10 9.90±5.73 9.30 57.87 2.04
单粒种子重SW (g) 0.04 0.51 0.19±0.07 0.18 35.73 2.03
囊衣及汁胞壁重SJW (g) 1.61 99.63 15.88±12.23 12.78 76.98 1.75
可溶性固形物TSS (%) 6.50 16.30 11.39±1.44 11.40 12.65 2.06
可滴定酸TA (g/100 mL) 0.11 2.91 0.81±0.49 0.67 60.24 1.86
固酸比TSS/TA 3.32 110.29 19.87±13.70 17.15 68.93 1.75
抗坏血酸AA (mg/100 mL) 9.79 70.21 29.49±9.34 27.73 31.68 1.88
果皮硬度PH (N) 1.24 25.18 6.48±3.70 5.75 57.16 1.84
果皮颜色PC (°) 33.69 84.42 56.62±9.22 56.32 16.28 2.08
果肉颜色FC (°) 50.76 88.67 68.21±6.39 67.45 9.36 2.02
花瓣长PEL (cm) 0.64 2.24 1.35±0.31 1.27 23.23 1.93
花瓣宽PEW (cm) 0.31 1.13 0.58±0.14 0.56 24.87 1.97
花药长AL (cm) 0.10 0.49 0.23±0.05 0.22 23.38 1.94
花药宽AW (cm) 0.01 0.11 0.11±0.02 0.11 19.95 1.71
平均值Mean — — — — 34.95 1.93

Fig. 1

Correlation analysis between fruit traits of mandarin germplasm resources"

Table 4

Correlation analysis of fruit and flower traits in mandarin"

性状
Traits		 花瓣长度
PEL		 花瓣宽度
PEW		 花药长度
AL		 花药宽度
AW		 单果重
FW		 果实横径
FD		 果实纵径
FL		 果形指数
FSI		 果皮厚度
PT		 单果皮重
PW		 囊瓣数
SNPF		 囊衣及汁
胞壁重
SJW
花瓣长度PEL 1
花瓣宽度PEW 0.72** 1
花药长度AL 0.37** 0.40** 1
花药宽度AW 0.27** 0.31** 0.61** 1
单果重FW 0.52** 0.51** 0.47** 0.33** 1
果实横径FD 0.53** 0.50** 0.43** 0.32** 0.97** 1
果实纵径FL 0.48** 0.47** 0.45** 0.29** 0.94** 0.90** 1
果形指数FSI -0.05 0.03 0.19** 0.05 0.23** 0.10 0.48** 1
果皮厚度PT 0.28** 0.28** 0.24** 0.10 0.43** 0.45** 0.42** 0.07 1
单果皮重PW 0.51** 0.49** 0.46** 0.30** 0.91** 0.91** 0.85** 0.15 0.67** 1
囊瓣数SNPF 0.29** 0.24** 0.20** 0.18* 0.32** 0.36** 0.18* -0.34** 0.15* 0.30** 1
囊衣及汁胞壁重SJW 0.53** 0.48** 0.38** 0.34** 0.90** 0.90** 0.83** 0.11 0.35** 0.82** 0.34** 1

Fig. 2

Cluster analysis of fruit quantitative traits based on mandarin germplasm resources"

Fig. 3

Comparison of important quality traits of 7 groups of mandarin Different letters represent significant differences between different groups (P<0.05)"

Table 5

Information on important agronomic traits of excellent mandarin germplasm"

品种名称
Name		 杂交组合
HC		 单果重
FW		 果形指数
FSI		 种子数
SNF		 可溶性固形物
TSS		 可滴定酸
TA		 固酸比
TSS/TA		 果皮硬度
PH		 抗坏血酸
AA		 果皮颜色
PC
LP31 西之香×金葵
Nishinokaori×Jin Kui		 104.44 1.09 1 12.70 0.48 26.46 7.16 62.63 44.59
LP45 西之香×金葵
Nishinokaori×Jin Kui		 131.18 0.91 3 13.20 0.42 31.43 11.45 56.10 38.84
LP18 红美人×美国糖桔
Benimadona×America Tang Ju		 104.40 0.91 1 13.80 0.57 24.21 9.66 52.15 33.69
LP3 塔罗科血橙×金葵
Tarocco Blood Orange×Jing Kui		 165.38 1.08 2 13.40 0.37 36.22 11.26 36.59 44.24
参试种质均值
AVTG		 - 102.84 0.81 9.90 11.39 0.81 19.87 6.48 29.49 56.62

Fig. 4

Phylogenetic tree analysis of mandarin germplasm resources"

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