青鱼生长QTL紧密连锁分子标记与生长性状的关联分析

杨琳; 郭加民; 王元浩; 周思扬; 李家乐; 徐晓雁; 沈玉帮

doi:10.7541/2024.2023.0414

青鱼生长QTL紧密连锁分子标记与生长性状的关联分析

杨琳^1,,
郭加民¹,
王元浩¹,
周思扬¹,
李家乐^{1, 2},
徐晓雁^{1, 2},
沈玉帮^{1, 2, ,}

1.
上海海洋大学农业农村部淡水水产种质资源重点实验室, 上海 201306
2.
上海海洋大学上海水产养殖工程技术研究中心, 上海 201306

基金项目: 国家现代农业产业技术体系项目(CARS-45)资助

详细信息

作者简介:
杨琳(1998—), 女, 硕士研究生; 研究方向为青鱼遗传育种与苗种工程。E-mail: yanglin11y@126.com

通信作者:
沈玉帮(1981—), 副教授; E-mail: ybshen@shou.edu.cn

中图分类号: S961.6
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- 文章访问数: 166
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出版历程
- 收稿日期: 2023-12-16
- 修回日期: 2024-03-04
- 网络出版日期: 2024-04-14
- 刊出日期: 2024-08-14

CORRELATION ANALYSIS OF GROWTH QTL TIGHTLY LINKAGE MOLECULAR MARKERS AND GROWTH TRAITS IN BLACK CARP (MYLOPHARYNGODON PICEUS)

YANG Lin^1,,
GUO Jia-Min¹,
WANG Yuan-Hao¹,
ZHOU Si-Yang¹,
LI Jia-Le^{1, 2},
XU Xiao-Yan^{1, 2} and
SHEN Yu-Bang^{1, 2, ,}

1.
Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
2.
Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China

Funds: Supported by the China Agriculture Research System (CARS-45)

Corresponding author:

摘要

摘要:
研究对前期建立的青鱼(Mylopharyngodon piceus)家系高密度遗传连锁图谱及体长QTL的定位结果进行深入分析, 在10号连锁群上识别到与体长相关的QTL区域, 存在2个与体长强烈相关的紧密连锁SNP位点。研究利用特异性标记判定青鱼遗传性别, 对SNP位点侧翼序列PCR扩增子进行sanger测序。得到准确的SNP位点基因型信息后, 研究对紧密连锁SNP位点不同基因型与邗江青鱼群体生长性状进行了细致的关联分析。结果表明, 在563尾邗江青鱼群体中, 雌鱼290尾, 雄鱼273尾, 雌雄比约为1.06﹕1。遗传分析显示, SNP₇₉₅₇G>C和SNP₉₈₀₂T>A有效等位基因数(N_e)分别为1.754和1.399, 观测杂合度(H_o)分别为0.384和0.266, 期望杂合度(H_e)分别为0.430和0.285, 多态信息含量分别(PIC)为0.508和0.378。相比雄鱼, 雌鱼生长速度更快, 但是变异系数更高, 说明雌鱼生长性状离散程度更大。SNP₇₉₅₇G>C和SNP₉₈₀₂T>A不同基因型在群体体长性状中存在显著差异。SNP₇₉₅₇G>C位点的GG基因型在雄鱼体长性状中具有显著优势(P<0.05), SNP₇₉₅₇G>C和SNP₉₈₀₂T>A单标记其他基因型与生长性状之间存在差异, 但未达到统计学差异。在SNP位点不同基因型构建的二倍型中, 雌雄个体表现出一定的生长差异, D8(GGTA)在生长方面具有显著优势 (P<0.05), 具有一定育种价值。研究结果可为选育快速生长青鱼新品种提供分子标记, 为未来青鱼遗传改良和分子标记辅助育种策略提供科学依据。
- SNP /
- 生长性状 /
- 关联分析 /
- 青鱼
Abstract:
In this study, leveraging the high-density genetic linkage map and growth QTL mapping outcomes established in the prior phase for black carp (Mylopharyngodon piceus), two SNPs loci were identified as correlated with growth traits within the Hanjiang population of black carp. These loci were situated on LG10 (linkage group) and closely associated with a specific growth QTL. Sex-specific markers were devised for sex determination. Subsequently, SNP polymorphisms were assessed through direct sequencing, and the association degree of different genotypes with male and female growth traits was scrutinized. The results showed that among the 563 individuals in the Hanjiang black carp population, there were 290 females and 273 males, with a female-to-male ratio of approximately 1.06:1. Genetic diversity analyses showed that the effective number of alleles (N_e) was 1.754 and 1.399, observed heterozygosity (H_o) was 0.384 and 0.266, expected heterozygosity (H_e) was 0.430 and 0.285, and polymorphic information content (PIC) was 0.508 and 0.378 for SNP₇₉₅₇G>C and SNP₉₈₀₂T>A, respectively. Compared to males, females exhibited faster growth rates, albeit with higher coefficients of variation, indicating greater variability in females growth traits. Genotypes of SNP₇₉₅₇G>C and SNP₉₈₀₂T>A displayed significant disparities in body length traits within the black carp population. The SNP₇₉₅₇G>C GG genotype notably dominanted (P<0.05) in male body length traits, while variations in haplotypes between SNP₇₉₅₇G>C and SNP₉₈₀₂T>A showed distinctions in growth traits, albeit not reaching statistical difference. Among diplotypes constructed from the two SNP loci, males and females showed dissimilarities in growth, with D8 (GGTA) notably superior in growth traits (P<0.05). The results of this study provide potential molecular markers for selective breeding of new fast-growing black carp varieties and establish a theoretical foundation for the in-depth exploration of growth traits fine mapping in black carp, along with QTL tightly linked marker assisted selected breeding.
- SNP /
- Growth traits /
- Correlation analysis /
- Mylopharyngodon piceus

HTML全文

图 1 遗传性别分子标记基因分型结果

Figure 1. The genotyping results of genetic sex markers

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图 2 SNP位点测序峰图

Figure 2. The sequencing peak chart of SNPs site

下载: 全尺寸图片幻灯片

表 1 SNP分子标记的引物信息

Table 1 Primer sequences of SNP molecular markers

标记名称 Marker name	引物序列 Primer sequence (5′—3′)	退火温度 T_m (℃)	产物大小 Size (bp)
SNP₇₉₅₇	TCATAGCCTTTCCCTGC	56	221
SNP₇₉₅₇	CTCTGTCGTTCCTTATTTACTC	56	221
SNP₉₈₀₂	ACTGGTTTGATTTGGGAC	54	409
SNP₉₈₀₂	GGCAACAGACAAGTGACC	54	409

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表 2 邗江青鱼群体中2个SNP位点的遗传参数

Table 2 Genetic parameters of 2 SNP loci in Hanjiang population of black carp

SNP 位点 SNP locus	有效等位基因数 N_e	观测杂合度 H_o	期望杂合度 H_e	多态信息量 PIC	Hardy- Weinberg 平衡 P_HW
SNP₇₉₅₇G>C	1.754	0.384	0.430	0.508	0.011
SNP₉₈₀₂T>A	1.399	0.266	0.285	0.378	0.118

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表 3 邗江青鱼群体生长表型数据

Table 3 Phenotypic data in Hanjiang population of black carp

性状 Trait	极小值 Minimum		极大值 Maximum		均值 Mean±SD			变异系数 Coefficient of variation
性状 Trait	雌 Female	雄 Male	雌 Female	雄 Male	群体 Population	雌 Female	雄 Male	群体 Population	雌 Female	雄 Male
体重 Body weight (g)	73.20	101.60	4250.00	3015.00	646.79±322.35	677.26±372.71	614.41±255.83	49.84%	55.03%	41.64%
体长 Body length (cm)	23.40	21.10	61.20	56.30	32.71±4.36	33.26±4.54	32.12±4.09	13.31%	13.65%	12.73%

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表 4 邗江青鱼群体的基因型及等位基因频率统计

Table 4 Genotype and allele frequency of SNP site in Hanjiang population of black carp

SNP位点 SNP site	基因型频率 Genotype frequency			等位基因频率 Allele frequency
SNP₇₉₅₇G>C	GG	GC	CC	G	C
SNP₇₉₅₇G>C	0.50(279)	0.38(216)	0.12(68)	0.69	0.31
SNP₉₈₀₂T>A	TT	TA	AA	T	A
SNP₉₈₀₂T>A	0.69(391)	0.27(150)	0.04(22)	0.83	0.17

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表 5 SNP位点与体重和体长性状的关联分析(平均值±标准差)

Table 5 Association of SNPs with growth trait of Hanjiang population of black carps (mean±SD)

位点 Locus	基因型 Genotype	个体数/尾 Number	体重 Body weight (g)	体长 Body length (cm)
SNP₇₉₅₇G>C	GG	279	664.34±272.53	33.04±4.03^a
	GC	216	640.72±398.71	32.58±4.69^ab
	CC	68	594.01±225.02	31.75±4.45^b
SNP₉₈₀₂T>A	TT	391	633.43±348.52	32.45±4.43^b
	TA	150	685.57±248.36	33.37±3.96^a
	AA	22	619.78±278.45	32.87±5.27^ab
注: 同位点同列数据字母不同表示差异显著(P<0.05); 下同Note: Different letters in the same site and column show significant difference (P<0.05); the same applies below

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表 6 不同性别个体中2个SNP位点与生长性状的关联分析(平均值±标准差)

Table 6 Association of 2 SNP with growth trait in individuals of different sexes (mean±SD)

位点 Locus	基因型 Genotype	雌鱼Female			雄鱼Male
位点 Locus	基因型 Genotype	个体数/尾 Number	体重 Body weight (g)	体长 Body length (cm)	个体数/尾 Number	体重 Body weight (g)	体长 Body length (cm)
SNP₇₉₅₇G>C	GG	146	678.71±242.30	33.31±3.88	133	648.57±302.41	32.75±4.18^a
	GC	109	689.30±520.94	33.36±5.25	107	591.24±202.59	31.78±3.92^ab
	CC	35	633.72±256.73	32.72±4.77	33	551.88±180.09	30.73±3.89^b
SNP₉₈₀₂T>A	TT	197	666.67±411.08	33.06±4.57	194	596.60±270.26	31.83±4.21
	TA	81	714.33±286.07	33.74±4.48	69	651.81±191.68	32.94±3.22
	AA	12	600.98±157.98	33.38±4.39	10	642.34±386.49	32.26±6.35

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表 7 SNP₇₉₅₇G>C和SNP₉₈₀₂T>A位点组成的二倍型和生长性状的关联分析(平均值±标准差)

Table 7 Analysis of Diplotypes of SNP₇₉₅₇G>C and SNP₉₈₀₂T>A with growth traits (mean±SD)

二倍型 Diplotypes	SNP 位点 SNP locus		体重 Body weight (g)			体长 Body length (cm)
二倍型 Diplotypes	SNP₇₉₅₇	SNP₉₈₀₂	群体 Population	雌 Female	雄 Male	群体 Population	雌 Female	雄 Male
D1	CC	TT	583.56± 221.66^b(62)	619.60± 259.70(29)	551.88± 180.09^b(33)	31.62± 4.38^b(62)	32.63± 4.74(29)	30.73± 3.89^b(33)
D2	CC	TA	677.58± 274.28^ab(5)	677.58± 274.27(5)	*(0)	32.66± 5.86^ab(5)	32.66± 5.86(5)	*(0)
D3	CC	AA	*(1)	*(1)	*(0)	*(1)	*(1)	*(0)
D4	GC	TT	659.98± 478.66^ab(139)	718.89± 619.20(73)	594.82± 231.37^ab(66)	32.59± 5.24^b(139)	33.37± 5.81(73)	31.73± 4.41^b(66)
D5	GC	TA	622.74± 188.29^b(59)	646.56± 223.24(27)	602.65± 153.70^ab(32)	32.72± 3.28^ab(59)	33.29± 3.66(27)	32.24± 2.89^ab(32)
D6	GC	AA	550.99± 130.34^b(18)	577.54± 151.22(9)	524.43± 107.93^ab(9)	32.01± 4.29^ab(18)	33.52± 4.88(9)	30.49± 3.18^b(9)
D7	GG	TT	630.28± 257.20^b(190)	640.91± 187.39(95)	619.64± 312.51^ab(95)	32.61± 3.74^b(190)	32.94± 3.30(95)	32.27± 4.14^ab(95)
D8	GG	TA	729.14± 275.20^a(86)	755.42± 314.14(49)	694.33± 212.24^a(37)	33.86± 4.24^a(86)	34.10± 4.80(49)	33.55± 3.41^a(37)
D9	GG	AA	*(3)	*(2)	*(1)	*(3)	*(2)	*(1)
注: 括号内为个体数, 小于或等于3用号表示Note: Number of individuals is in parentheses, indicates the number is less than or equal to 3

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