形态学和SNP标记分析马氏珠母贝杂交子代及其亲本群体的遗传结构

doi:10.11978/2019012

Abstract

Abstract:

The pearl oyster, Pinctada fucata martensii, is a primary marine bivalve species. To study the genetic structure and relationship of cultured parents and their hybrid generation, external morphology and genetic structure were assessed in the three populations of P. fucata martensii from Shenzhen population (female), Hainan population (male) and their hybrid generation F1, based on morphological multivariate analysis and SNP markers. The results showed that the average discriminant accuracy was 72%, and the morphological characteristics of F1 and female were similar, while male was the most different from the other two populations. Four SNP markers of the three populations were genotyped by the HRM (high resolution melting) method. The results showed that the average observed (H_o) and expected (H_e) heterozygosity were 0.2110 to 0.2879 and 0.3317 to 0.4685, respectively; and the heterozygosity of F1 was higher than that of the parent populations. The average polymorphism information content (PIC) values of the three populations were in the range of 0.2643 to 0.3556, which showed moderate genetic diversity. Gene flow (N_m) between F1 and female was the largest (7.7701), with minimum genetic distance being 0.0546; thus, their genetic relationships were similar. Gene flow (N_m) between the parent populations was minimum (1.9662), with largest genetic distance being 0.1759. Finally, we found that rs8 marker can be used as a specific marker to discriminate parent populations. These results should assist the discriminate of genetic structure and management of selective breeding of P. fucata martensii.

Key words: Pinctada fucata martensii, genetics, genetic structure, morphology, SNP

HUANG Jing, PAN Xiaolan, XU Meng, LIU Wenguang, ZHANG Hua, HE Maoxian. Morphological and SNP markers for analysis of genetic structure of hybrid progeny and their parental populations of Pinctada fucata martensii[J].Journal of Tropical Oceanography, 2019, 38(6): 80-89.

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位点名称	序列(5'-3')	SNP 类型	退火温度/℃	对应产物长度/bp
rs8	F: CCCAGCATACTTTATGGCAGAAT R: CCTAGCGTGGAGAAGAGATGTA	T/C	55	122
rs33	F: CAATACTCTCAGGGACATCTT R: CTCAACAGTGTCGCTTATATG	A/G	50	107
rs35	F: TTCCGCAGGATGAATTTAGGT R: TCTGAAGTCTGTTTGTCCAATG	C/A	53	103
rs44	F: CCAAAGCCAACTACACCCAAA R: GTCAAACGCCCACGATACAC	C/A	55	144

性状	父本	F1	母本
壳长	58.25±5.58^a	56.40±5.20^a	56.52±4.29^a
壳宽	23.44±2.23^a	20.23±2.84^b	21.72±2.43^ab
壳高	59.24±5.10^a	55.60±5.47^b	56.25±4.45^b
铰合线	51.16±3.79^a	50.17±4.97^a	50.84±4.28^a
总重	28.16±6.07^a	24.60±7.49^b	24.12±5.33^b
壳重	14.23±2.78^a	13.11±3.78^ab	11.95±2.62^b
软体部重	10.77±3.25^a	8.81±3.38^b	8.49±2.64^b
壳宽指数	0.17±0.01^a	0.15±0.01^b	0.16±0.01^ab
壳重指数	18.12±2.75^b	20.42±2.06^a	17.43±2.60^b
肥满度指数	13.36±2.27^a	13.28±2.53^a	13.02±2.25^a
壳高/壳长	1.02±0.05^a	0.99±0.05^b	1.00±0.06^ab
壳宽/壳长	0.41±0.03^a	0.36±0.03^b	0.38±0.03^ab
铰合线/壳长	0.88±0.05^b	0.89±0.05^ab	0.90±0.05^a

性状	负荷值
性状	主成分1	主成分2	主成分3
总重	0.969*	0.019	-0.040
软体部重	0.954*	0.021	0.107
壳高	0.937*	-0.052	-0.030
壳重	0.932*	-0.027	-0.103
铰合线长	0.901*	0.064	0.069
壳长	0.884*	0.067	-0.433
壳宽指数	0.113	0.952*	0.173
壳宽	0.301	0.938*	0.061
壳宽/壳长	0.102	0.936*	0.250
壳重指数	0.184	-0.758	0.088
肥满度	0.454	-0.531	0.393
铰合线/壳长	0.089	0.003	0.846*
壳高壳/长	0.250	-0.238	0.688*
贡献率/%	43.2	27.6	12.8

群体	数量	预测分类			判别准确率		综合判别率
群体	数量	父本	F1	母本	P1	P2	综合判别率
父本	50	36	9	5	72%	75%	72%
F1	50	8	32	10	64%	68.1%
母本	50	4	6	40	80%	72.7%

群体名称	位点	I	H_o	H_e	PIC	HWE P值
父本	rs8	0.3768	0.2500	0.2222	0.1948	0.4527
	rs33	0.6809	0.3438	0.4955	0.3685	0.0780
	rs35	0.3111	0.0625	0.1726	0.1555	0.0044*
	rs44	0.6211	0.1875	0.4365	0.3384	0.0010*
平均值		0.4975	0.2110	0.3317	0.2643
F1	rs8	0.6002	0.1515	0.4163	0.3260	0.0003*
	rs33	0.6816	0.3030	0.4960	0.3692	0.0230
	rs35	0.5860	0.4242	0.4028	0.3182	0.7500
	rs44	0.6635	0.2727	0.4779	0.3598	0.0120
平均值		0.6328	0.2879	0.4483	0.3433
母本	rs8	0.6881	0.4333	0.5034	0.3724	0.4380
	rs33	0.5799	0.3333	0.3977	0.3137	0.3622
	rs35	0.6657	0.0333	0.4808	0.3614	0.0000*
	rs44	0.6926	0.2333	0.4921	0.3747	0.0025*
平均值		0.6566	0.2583	0.4685	0.3556

Morphological and SNP markers for analysis of genetic structure of hybrid progeny and their parental populations of Pinctada fucata martensii

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群体名称	基因型(频率)
群体名称	rs8	rs33	rs35	rs44
父本	TT(0.75)	GG(0.41)	CC(0.88)	CC(0.59)
	TC(0.25)	GA(0.34)	CA(0.06)	CA(0.19)
	CC(0)	AA(0.25)	AA(0.06)	AA(0.22)
F1	TT(0.64)	GG(0.27)	CC(0.52)	CC(0.24)
	TC(0.15)	GA(0.30)	CA(0.42)	CA(0.27)
	CC(0.21)	AA(0.42)	AA(0.06)	AA(0.49)
母本	TT(0.23)	GG(0.10)	CC(0.60)	CC(0.37)
	TC(0.43)	GA(0.33)	CA(0.03)	CA(0.23)
	CC(0.33)	AA(0.57)	AA(0.37)	AA(0.40)

	遗传距离和遗传相似系数			基因流和遗传分化系数
	父本	F1	母本	父本	F1	母本
父本	****	0.9320	0.8387	****	0.0546	0.1128
F1	0.0704	****	0.9947	4.3262	****	0.0166
母本	0.1759	0.0546	****	1.9662	7.7701	****