| Oysters are some kind of the most important aquaculture species with the highest yield. Recently, massive summer mortality in oysters has been observed around the world. It has been reported that high water temperature is one of the key factors resulting in the massive summer mortality in oysters. As growth and survive are the most important factors affecting the yield of oysters, dissecting the genetic mechanism of them and then directing the genetic improvement is the urgent need of the oyster culture industry. The present study performed SNP calling with highthroughput sequencing technology, genetic mapping of growth-related and thermotolerant traits, and identifying SNP markers and genes associated with these traits. The results provided valueable genetic resources for marker-assisted breeding and dissecting the genetic mechnism of the economically important traits in oysters. 1 Construction of dense linkage mapThe present study built a hybrid family of Crassostrea gigas gigas and Crassostrea gigas angulata which were distributed in north and south coast of China separately. The present study constructed a dense linakge map for oysters. For the sexaverage map, 1,694 markers fell into 10 linkage groups(the linkage groups were named A1–A10). For the female linkage map, 1,102 markers fell into 12 linkage groups(the linkage groups were named F1–F10). For the male linkage map, 689 markers fell into 12 linkage groups(the linkage groups were named M1–M10). The sex-average map spanned a total genetic distance of 1084.3 cM, with an average spacing of 0.8 cM and a Coa of 98.7%. The female map spanned a total genetic distance of 1034.6 cM, with an average spacing of 1.3 cM and a Coa of 97.5%. The male map spanned a total genetic distance of 744.8 cM, with an average spacing of 1.7 cM and a Coa of 95.2%. We observed an overall female-to-male recombination ratio of 1.39:1. The largest recombination ratio between sexes was found for linkage group 4, with a female:male ratio of 2.40:1, and the smallest recombination ratio between sexes was found for linkage group 9, with a female:male ratio of 1.07:1. Localized differences in recombination rates between the sexes were observed. Of the 1,694 markers on the sex-average map, 836(49.4%) showed significant(P < 0.05) segregation distortion. For the sex-average linkage map, LG A8 and LG A5 presented the most severe segregation distortion, with 77.2% and 73.5% of markers distorted, respectively. LG A10 presented the lowest segregation distortion, with 12.4% of markers distorted. Distorted markers tended to be clustered, rather than randomly distributed across a linkage group For the distorted markers in the lmxll type(423), 183 showed homozygote deficiency while 240 showed heterozygote deficiency. For the distorted markers in the nnxnp type(238), 120 showed homozygote deficiency while 118 showed heterozygote deficiency. 2 Genetic mapping for growth-related traitsA total of 27 QTLs were identified, including seven for shell height, three for shell length, 10 for shell width, one for mass weight, and six for soft tissue weight. These 27 QTLs were distributed across eight linkage groups on the sex-average map, except for LG A3 and LG A6. More than half(16) of the QTLs were clustered in their respective LGs. The phenotypic variance explained by these QTLs ranged from 4.2% to 7.7%, with an average of 5.4%. The low phenotypic variance explained by these QTLs indicated that no major loci(explaining >20% of the total variation) were detected. For shell height, the seven QTLs explained 35.3% of the total phenotypic variance. For shell length, the three QTLs explained 20.1% of the total phenotypic variance. For shell width, the 10 QTLs explained 50.8% of the total phenotypic variance. For mass weight, the QTL explained 7.7% of the total phenotypic variance. For soft tissue weight, the six QTLs explained 34.1% of the phenotypic variance. A number of genes related to growth-related traits were identified from the higher-density map based on the Pacific oyster genome assembly. As shown, 38 annotated genes were identified in the QTL regions. Among the annotated genes, two were found to be growth-related(agl and fbp1), which function as key factors in carbohydrate metabolism, and others were found to participate in the assembly and regulation of the actin cytoskeleton(avil, fmn2, and specc1l), signal transduction pathways(prkg1, dusp6, and grk1), and the regulation of cell differentiation and development(tbata and megh8). 3 Genetic mapping for thermo-tolerant traitThe present study built a hybrid population of C. gigas gigas and C. gigas angulata and obtained two bulks of oyster with thermo-sensitive and thermo-tolerant traits by man-made heat stress. By whole genome resequencing, a total of 6,389,699 SNPs were identified in the thermo-tolerant bulk and 6,516,028 SNPs were identified in the thermo-susceptive bulk. SNPs identified in both pools(3,497,748) were used to calculate frequency difference. After filtering the depth of SNPs(with depth between 30-100 fold remained), 1,790,801 SNPs were retained. Those with frequency difference bigger than 0.4 were assumed as candidate SNPs. The average of frequency difference of all SNPs within the slide window was used as the Fst value of the slide window. The window size was set as 100 kb and the step wise as 10 kb. The biggest Fst value was 0.33 and the least Fst value was 0.1. The top 5% windows were selected as candidate windows. A total of 95 SNPs were identified as candidate SNPs and 48 genes as candidate genes by combining the data from transcription profile after heat stress of oyster. The verification of candidate SNPs was performed in nine oysters. The degree of thermo-tolerance of these nine oysters was identified by man-made heat stress. Finally, five SNPs from the bulks analysis were verified. However, none of SNPs from the transcription profile data was verified.A total of 15 HSP genes were quantified with quantitative PCR(qPCR) to map eQTLs controling their expression. However, only three of them presented differential expression among the mapping population. The eQTL mapping of the three genes detected two QTLs in total and 20 candidate genes were identified in the QTL regions. Of the candidate genes, forkhead box gene was reported to play an important role in cell under heat stress. The expression of forkhead box gene was regulated by the heat shock transcription factor(HSF). The forkhead box gene improved the ability of the cell to survive under heat stress. And forkhead box gene regulated the expression of HSP70 genes. The forkhead box genes was located in a slide window with a near value of Fst with the top 5% window. Our result implied that forkhead box gene may influence the thermo-tolerance of oysters by affecting the expression level of HSP genes. |
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