Genetic Diversity Analysis of Citri Fructus Germplasm Resources Based on Phenotypic Traits and SSR Markers

doi:10.13560/j.cnki.biotech.bull.1985.2025-0846

Abstract

Abstract:

Objective Citri fructus germplasm resources in China were investigated to analyze phenotypic variation of fruit traits, genetic diversity, population structure and genetic differentiation characteristics, providing a scientific basis for germplasm conservation and superior cultivar breeding. Method The total of 40 batches of fruits and 90 leaves samples of plants from 16 provinces (37 cities) of China were used as the test materials, and then the genetic diversity analysis was conducted using 15 phenotypic traits and screened 10 pairs of SSR markers. Result The Shannon-Wiener index H and Simpson’s diversity index D of 7 quality traits of citri fructus from different regions varied from 0.526 to 1.365 and 0.349 to 0.711, respectively. Among the 8 quantitative traits coefficient of variation ranged from 21% (number of segments) to 99% (single-fruit weight). According to phenotypic traits, the tested materials could be divided into three groups: Ⅰ (Xiangyuan and Zhique), Ⅱ (Xiangpao) and Ⅲ (Juyuan). The 10 pairs of primers with good polymorphism and stable bands were screened for PCR of SSR primers. The results showed that tthe number of alleles (Na), the number of effective alleles (Ne), Shannon’s diversity index (I), observed heterozygosity (Ho), and expected heterozygosity (He) at the locus level were 1.832, 1.354, 0.331, 0.824, and 0.210, respectively. By clustering, population structure and PCoA analysis, the 90 germplasm were divided into four groups. Xiangyuan and Zhique were further separated. The genetic diversity of the four groups was different with the descending order of Zhique (Ho=0.682, He=0.199), Juyuan (Ho=0.659, He=0.175), Xiangpao (Ho=0.436, He=0.133) and Xiangyuan (Ho=0.391, He=0.127). The Mantel test showed that the genetic distance of the citri fructus and geographical distance of the provenances were significantly correlated (r=0.558, P=0.010). The molecular variance analysis of xiang yuan population exhibited 73% of the variation within the population. Conclusion Citri fructus germplasm resources in China have rich phenotypic genetic variation and high diversity.

Key words: citri fructus, germplasm resource, phenotypic identification, cluster analysis, genetic diversity

WEI Li-na, JIANG Jing-long, DENG Xi-xi, LI Yan, LI Li, DENG Jia-rui, DING De-kuan. Genetic Diversity Analysis of Citri Fructus Germplasm Resources Based on Phenotypic Traits and SSR Markers[J]. Biotechnology Bulletin, 2026, 42(4): 202-215.

Figures/Tables 20

References 35

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质量性状 Quality trait	性状描述及分级 Character description and classification
质量性状 Quality trait	1	2	3	4	5	6
平滑度 Peel smoothness	光滑 Smooth	较光滑 Slightly smooth	粗糙 Rough
果实形状 Fruit shape	类球形 Spheroid	高扁圆形 High oblate	倒卵圆形 Obovoid	纺锤形 Fusiform
果顶形状 Apex shape	凸 Protruding	浅凹 Slightly depressed	平 Flatten	乳突 Mammillated	圆 Rounded
果顶印圈 Areole ring	明显 Obvious	不明显 Indistinct	无 None
果基形状 Base shape	深凹 Depressed	凸 Protruding	浅凹 Slightly depressed	平 Flatten	圆 Rounded	颈领 Necked
外果皮颜色 Peel color	黄色 Yellow	淡黄 Pale yellow	黄绿 Green-yellow	橙红 Orange-red	橙黄 Orange-yellow
白皮层颜色 Albedo color	白色 White	淡黄 Pale yellow

质量性状 Quality trait	性状描述及分级 Character description and classification
质量性状 Quality trait	1	2	3	4	5	6
平滑度 Peel smoothness	光滑 Smooth	较光滑 Slightly smooth	粗糙 Rough
果实形状 Fruit shape	类球形 Spheroid	高扁圆形 High oblate	倒卵圆形 Obovoid	纺锤形 Fusiform
果顶形状 Apex shape	凸 Protruding	浅凹 Slightly depressed	平 Flatten	乳突 Mammillated	圆 Rounded
果顶印圈 Areole ring	明显 Obvious	不明显 Indistinct	无 None
果基形状 Base shape	深凹 Depressed	凸 Protruding	浅凹 Slightly depressed	平 Flatten	圆 Rounded	颈领 Necked
外果皮颜色 Peel color	黄色 Yellow	淡黄 Pale yellow	黄绿 Green-yellow	橙红 Orange-red	橙黄 Orange-yellow
白皮层颜色 Albedo color	白色 White	淡黄 Pale yellow

引物名称 Primer name	正向引物序列 Forward primer （5′‒3′）	反向引物序列 Reverse primer （5′‒3′）	退火温度 Tm （℃）
Cs2	TCCACAAGGAGAAGAAACGG	GCGTCTTTACTGTTACCGGG	56
Cs3	GTTGCGCAGTTATTCTCAAA	CCGACCACTTTTACCCACTG	54
Cs6	AGGTCTACATTGGCATTGTC	ACATGCAGTGCTATAATGAATG	52
Cs9	TAAAAACCAACGTCCCCTCA	CGGGCGAGGTAGAAGTAATG	54
Cs11	CGCAAATGACTTCCCAGAAT	GCTCCCTCCGATTCTCTCTC	52
Cs13	CACGCAGCTTGAGTTTGAAG	GTGCCGTTTAGGGTTTTCCT	55
Cs14	CAGGCAGTAACCTCCCAGAC	AGCGAAAGCTAATGATGGTG	54
Cs15	CGGGCTAGGCTGAGAGATA	TTCTTTGGAGCCGAACAACT	52
Cs20	AGTGAACTGTCCATTGGATTTTCG	GTGTTGAATCCCGACCTTCTACC	54
Cs21	GCAGCGCAACAACATAACTA	GGCCAATAGCTTCCATTCA	52

引物名称 Primer name	正向引物序列 Forward primer （5′‒3′）	反向引物序列 Reverse primer （5′‒3′）	退火温度 Tm （℃）
Cs2	TCCACAAGGAGAAGAAACGG	GCGTCTTTACTGTTACCGGG	56
Cs3	GTTGCGCAGTTATTCTCAAA	CCGACCACTTTTACCCACTG	54
Cs6	AGGTCTACATTGGCATTGTC	ACATGCAGTGCTATAATGAATG	52
Cs9	TAAAAACCAACGTCCCCTCA	CGGGCGAGGTAGAAGTAATG	54
Cs11	CGCAAATGACTTCCCAGAAT	GCTCCCTCCGATTCTCTCTC	52
Cs13	CACGCAGCTTGAGTTTGAAG	GTGCCGTTTAGGGTTTTCCT	55
Cs14	CAGGCAGTAACCTCCCAGAC	AGCGAAAGCTAATGATGGTG	54
Cs15	CGGGCTAGGCTGAGAGATA	TTCTTTGGAGCCGAACAACT	52
Cs20	AGTGAACTGTCCATTGGATTTTCG	GTGTTGAATCCCGACCTTCTACC	54
Cs21	GCAGCGCAACAACATAACTA	GGCCAATAGCTTCCATTCA	52

质量性状 Quality trait	分级及频率 Classification and frequency （%）						Shannon-Wiener指数 Shannon-Wiener index H	Simpson指数 Simpson index D
质量性状 Quality trait	1	2	3	4	5	6	Shannon-Wiener指数 Shannon-Wiener index H	Simpson指数 Simpson index D
平滑度 Peel smoothness	30.0	50.0	20.0	-	-	-	1.030	0.620
果实形状 Fruit shape	35.0	37.5	17.5	10.0	-	-	1.277	0.696
果顶形状 Apex shape	30.0	12.5	40.0	15.0	2.5	-	1.365	0.711
果顶印圈 Areole ring	30.0	12.5	57.5	-	-	-	0.939	0.564
果基形状 Base shape	10.0	5.0	65.0	5.0	12.5	2.5	1.161	0.546
外果皮颜色 Peel color	65.0	12.5	12.5	2.5	7.5	-	1.084	0.540
白皮层颜色 Albedo color	77.5	22.5	-	-	-	-	0.526	0.349