Dataset Information

Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds.

ABSTRACT: Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.

SUBMITTER: Chessari G

PROVIDER: S-EPMC10762050 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds.

Chessari Giorgio G Criscione Andrea A Marletta Donata D Crepaldi Paola P Portolano Baldassare B Manunza Arianna A Cesarani Alberto A Biscarini Filippo F Mastrangelo Salvatore S

Scientific reports 20240102 1

Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighte ...[more]

PMID: 38168531

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Project description:Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5-2 Mb and 0.5-1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55-50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21-132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima's D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.

Project description:Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

Project description:BackgroundGoat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments. Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity, especially as we are facing important climate and agriculture challenges. To this aim the genomic architecture of 480 goats belonging to five breeds (i.e., Saanen [SAA], Camosciata delle Alpi [CAM], Murciano-Granadina [MUR], Maltese [MAL], Sarda [SAR]) reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits. Inbreeding, runs of homozygosity (ROH) and runs of heterozygosity (ROHet) were identified. Finally, candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.ResultsIn total, we detected 10,341 ROH in the SAA genome, 11,063 ROH in the CAM genome, 12,250 ROH in the MUR genome, 8,939 ROH in the MAL genome, and 18,441 ROH in the SAR genome. Moreover, we identified 4,087 ROHet for SAA, 3,360 for CAM, 2,927 for MUR, 3,701 for MAL, and 3,576 for SAR, with SAR having the highest heterozygosity coefficient. Interestingly, when computing the inbreeding coefficient using homozygous segment (FROH), SAA showed the lowest value while MAL the highest one, suggesting the need to improve selecting strategies to preserve genetic diversity within the population. Among the most significant candidate genes, we identified several ones linked to different physiological functions, such as milk production (e.g., DGAT1, B4GALT1), immunity (GABARAP, GPS2) and adaptation to environment (e.g., GJA3, GJB2 and GJB6).ConclusionsThis study highlighted the genetic diversity within and among five goat breeds. The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation, which might negatively impact the animal population. Conversely, high levels of ROHet might indicate regions of the genetic diversity, beneficial for breed health and resilience. Therefore, these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.

Dataset Information

Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds.

Publications

Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds.

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