The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events

Abstract Background Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types. Results The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction. Conclusions Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction.

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The Cytogenetics of the Water Buffalo: A Review

Animals ◽

10.3390/ani11113109 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3109

Author(s):

Alessandra Iannuzzi ◽

Pietro Parma ◽

Leopoldo Iannuzzi

Keyword(s):

Water Buffalo ◽

Mediterranean Area ◽

Bubalus Bubalis ◽

World Population ◽

River Buffalo ◽

African Continent ◽

Specific Chromosome ◽

Asian Continent ◽

Cytogenetic Studies ◽

Swamp Buffalo

The water buffalo (Bubalus bubalis), also known as the Asian buffalo, is an essential domestic bovid. Indeed, although its world population (~209 million heads) is approximately one-ninth that of cattle, the management of this species involves a larger human population than that involved with raising cattle. Compared with cattle, water buffalo have been understudied for many years, but interest in this species has been increasing, especially considering that the world population of these bovids grows every year—particularly that of the river buffalo. There are two genera of buffalo worldwide: the Syncerus (from the African continent), and the Bubalus (from the southwest Asian continent, Mediterranean area, southern America, and Australia). All species belonging to these two genera have specific chromosome numbers and shapes. Because of such features, the study of chromosomes is a fascinating biological basis for differentiating various species (and hybrids) of buffaloes and characterizing their karyotypes in evolutionary, clinical, and molecular studies. In this review, we report an update on essential cytogenetic studies in which various buffalo species were described from evolutionary, clinical, and molecular perspectives—particularly considering the river buffalo (Bubalus bubalis 2n = 50). In addition, we show new data on swamp buffalo chromosomes.

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Bubalus bubalis: A Short Story

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.570413 ◽

2020 ◽

Vol 7 ◽

Author(s):

Antonio Humberto Hamad Minervino ◽

Marco Zava ◽

Domenico Vecchio ◽

Antonio Borghese

Keyword(s):

Short Story ◽

Water Buffalo ◽

Bubalus Bubalis ◽

Data Sources ◽

Bison Bison ◽

River Buffalo ◽

Limited Information ◽

Worldwide Distribution ◽

The World ◽

Swamp Buffalo

The domestic buffalo (Bubalus bubalis), also known as water buffalo or Asian buffalo to prevent confusion with the American bison (Bison bison), wrongly named buffalo in North America, comprises two subspecies: the river buffalo (B. bubalis bubalis) and the swamp buffalo (B. bubalis kerebau). The swamp buffalo has a consistent phenotype and is considered as one type, even if many breeds are recognized within it; conversely, the river buffalo subspecies has many breeds. We found limited information available regarding the worldwide distribution of buffaloes. The best estimate is that 208,098,759 buffalo head are distributed in 77 countries in five continents. In this review, we presented the basic aspects of the water buffalo and unraveled the buffalo path followed from the origin of the species to its current global distribution. We reviewed several data sources to provide a better estimate of the world buffalo count and distribution.

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KUALITAS SPERMATOZOA ASAL CAPUT, CORPUS, DAN CAUDA EPIDIDIMIS PADA KERBAU RAWA (Bubalus bubalis carabenensis)

Jurnal Ilmu dan Teknologi Peternakan Tropis ◽

10.33772/jitro.v3i3.2575 ◽

2016 ◽

Vol 3 (3) ◽

pp. 97

Author(s):

Muhammad Riyadhi ◽

Akbar Budiansa ◽

Muhammad Rizal

Keyword(s):

Artificial Insemination ◽

Bubalus Bubalis ◽

Spermatozoa Motility ◽

Swamp Buffaloes ◽

Swamp Buffalo

The purpose of this research was evaluate the quality of spermatozoa concentration in the caput, corpus and cauda of the swamp buffalo epididymis (Bubalus bubalis carabanensis). Method of this research was to exploration to 13 epididymides of eight swamp buffaloes were obtained from Banjar and Banjarmasin slaughterhouses,evaluated the quality of spermatozoa in caput, corpus and cauda of epididymis. Quality of collected-spermatozoa including spermatozoa motility, percentage of live spermatozoa, spermatozoa concentration and percentage of abnormality. Result of this study showed that mean of each of caput spermatozoa motility, percentage of live spermatozoa, spermatozoa concentration and percentage of abnormality; 0%, 45.43% (31.87–72%), 189,62 x106 (40–480 x106) and 56.16 %(44.34–66.53%), corpus ;2.77% (1–9%), 58.73% (45.14 –76%), 152.31 x106 (45 – 345x106), and 47.61 %(23.92 – 60.15%), cauda;53.46% (20 – 70%), 74.32 % (56.68 – 83%), 1,459.62 x106 (825 – 2,340x106), and 34.60%(15.89 –50.04%). In conclusion, spermatozoaofcaudaepididymis could be used in artificial insemination program.Keywords: Spermatozoa, epididymis, swamp buffalo.

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Correction to: Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

BMC Genetics ◽

10.1186/s12863-020-00841-7 ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 1

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil Sarghale ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Bubalus Bubalis ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Inbreeding Coefficients ◽

Genome Wide ◽

Genome Wide Scan

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

BMC Genetics ◽

10.1186/s12863-020-0824-y ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 6

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil Sarghale ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Bubalus Bubalis ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Inbreeding Coefficients ◽

Genome Wide ◽

Genome Wide Scan

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

10.21203/rs.2.17561/v3 ◽

2020 ◽

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil Sarghale ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Muscle Development ◽

Bone Development ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Effective Population ◽

A Genome ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P≤0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

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THE KARYOTYPE OF THE AUSTRALIAN SWAMP BUFFALO (BUBALUS BUBALIS)

Canadian Journal of Genetics and Cytology ◽

10.1139/g76-014 ◽

1976 ◽

Vol 18 (1) ◽

pp. 101-104 ◽

Cited By ~ 5

Author(s):

G. L. Toll ◽

C. R. E. Halnan

Keyword(s):

Diploid Number ◽

Bubalus Bubalis ◽

River Buffalo ◽

Swamp Buffalo

The karyotype of the Asian Swamp buffalo has previously been reported for beasts of Thailand and Malaysia. A diploid number of 48 was observed which was different to that found for the River buffalo (2n = 50). This report describes the karyotype of Australian Swamp buffalo, which has proved in agreement with that of the Asian Swamp buffalo. An hypothesis is advanced to account for movement of buffalo down the island chain from Malaya to Australia.

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Major Histocompatibility Complex Dmα/β Genes and Their Expressional Diversity in Healthy and Diseased Water Buffalo Bubalus bubalis

Cellular Physiology and Biochemistry ◽

10.1159/000488618 ◽

2018 ◽

Vol 46 (2) ◽

pp. 505-519

Author(s):

Leena Rawal ◽

Deepak Panwar ◽

Sher Ali

Keyword(s):

Major Histocompatibility Complex ◽

Antigen Processing ◽

Water Buffalo ◽

Treatment Strategies ◽

Bubalus Bubalis ◽

Chromosome 2 ◽

Major Histocompatibility ◽

Specific Expression ◽

Histocompatibility Complex ◽

Mhc Locus

Background/Aims: The major histocompatibility complex (MHC) categorized into three (I, II and III) classes elicits the immunogenic response by presenting exogenous peptides to T cells. The MHC-II DM is composed of DMα and DMβ, two polypeptide chains, both are encoded by separate MHC genes involved in antigen processing and presentation. Despite the acknowledged role of MHC complex in humans, the literature is silent on the organization and expression of these genes in water buffalo Bubalus bubalis, an agriculturally important animal species. Methods: We deduced the full-length mRNA sequences of DMα and DMβ genes, localized them onto the chromosome 2, assessed their copy number per haploid genome and studied tissue and disease specific expression. Results: The Real Time PCR showed higher expression of both the genes and their seven interacting partners in spleen, gonads and spermatozoa. Significantly, upregulation of DMα and DMβ genes and their interacting partners were detected in diseased group of buffaloes as compared to that in healthy ones. Conclusion: The upregulation of Bubalus bubalis (BuLA)-DMα and DMβ genes and their interacting partners reflect their role in regulating immune responses towards the amelioration of diseases. Work on this line would enhance our understanding on the overall roles of MHC locus, allowing development of possible therapeutic treatment strategies.

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

10.21203/rs.2.17561/v5 ◽

2020 ◽

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil Sarghale ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Muscle Development ◽

Bone Development ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Effective Population ◽

A Genome ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P≤0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

10.21203/rs.2.17561/v1 ◽

2019 ◽

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil-Sarghaleh ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Muscle Development ◽

Bone Development ◽

Coat Colour ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Effective Population ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background: Consecutive homozygous fragments of the genome inherited from a common ancestor to offspring are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identifying genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P<0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial and/or natural selection.

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