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Outline
In this study， the objective of this study was to explore the functional candidate genes affecting the apparent digestibility of crude fiber in Suhuai pigs （25% of Suhuai pigs and 75% of Large White pigs）， so as to lay the foundation for the analysis of the genetic mechanism of the apparent digestibility of crude fiber in pigs. A total of 320 160-day-old Sohuai pigs were selected for the study， and the apparent digestibility was calculated by measuring the crude fiber content of feed and feces. At the same time， ear tissue samples were collected for 80K single nucleotide polymorphism （SNP） microarray typing， and 51 625 SNPs were retained after quality control， based on which the heritability was calculated and the microarray data were populated to the resequencing level. Subsequently， genome-wide association study （GWAS） was conducted based on the populated data， and Bayesian fine-tuning method was used for in-depth analysis. The results showed that the apparent digestibility of crude fiber in this population was 54.30%±1.03%， and the coefficient of variation was 33.87%， which showed a large phenotypic variation and certain space for selection and breeding. The heritability was calculated as 0.268±0.106 （P=0.012）， which is a medium heritability trait. GWAS （genome-wide association study） analysis identified 359 SNPs on chromosomes 4， 5， and 9 that were significantly associated with crude fiber apparent digestibility （P<3.30×10-6）. Three quantitative trait loci （QTL） region were identified by Bayesian fine localization on chromosome 4 （11.48-12.75 Mb）， chromosome 5 （83.39-84.86 Mb）， and chromosome 9 （18.81-19.68 Mb）. After comparison with the Pig QTL database， all of them were newly discovered QTL affecting the apparent digestibility of crude fiber in pigs. Six new functional candidate genes， MYC， ANO4， NR1H4，ACTR6， SCYL2 and DLG2， were identified through database and literature search， and PheWAS analysis of the candidate genes using the PigBiobank database of the FarmGTEx project showed that these genes were associated with daily weight gain， meat color and health of pigs. PheWAS analysis using the PigBiobank database of the FarmGTEx program revealed that these genes were significantly associated with the traits of daily weight gain， meat color and health. In this study， 3 QTLs and 6 functional candidate genes affecting crude fiber digestion in pigs were newly identified， which can be used as a reference for the study of genetic molecular mechanism and the implementation of molecular breeding for the trait of apparent digestibility of fiber.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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