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Evidence of Bos javanicus x Bos indicus hybridization and major QTLs for birth weight in Indonesian Peranakan Ongole cattle.

Hartati H, Utsunomiya YT, Sonstegard TS, Garcia JF, Jakaria J, Muladno M - BMC Genet. (2015)

Bottom Line: We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle.Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle.This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization.

View Article: PubMed Central - PubMed

Affiliation: Beef Cattle Research Station, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jln. Pahlawan no. 2 Grati, Pasuruan, East Java, 16784, Indonesia. hartati06@yahoo.com.

ABSTRACT

Background: Peranakan Ongole (PO) is a major Indonesian Bos indicus breed that derives from animals imported from India in the late 19(th) century. Early imports were followed by hybridization with the Bos javanicus subspecies of cattle. Here, we used genomic data to partition the ancestry components of PO cattle and map loci implicated in birth weight.

Results: We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle. Only two nearly fixed B. javanicus haplotypes were identified, suggesting that most of the B. javanicus variants are segregating under drift or by the action of balancing selection. The zebu component of the PO genome was estimated to derive from at least two distinct ancestral pools. Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle.

Conclusions: This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization. Additionally, previously described loci implicated in body size in worldwide beef cattle breeds also affect birth weight in PO cattle.

No MeSH data available.


Model-based clustering of cattle breeds assuming different numbers of ancestral populations (K). Each individual is represented by a vertical bar that can be partitioned into colored fragments with length proportional to cluster contribution. K = 4 approximates the ancestral European B. taurus, African B. taurus, B. indicus and B. javanicus populations. K = 7 distinguishes between the two zebu ancestors that generated GIR and NEL, and PO exhibits contributions from both ancestral populations. See Material and Methods for breed abbreviations
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Fig2: Model-based clustering of cattle breeds assuming different numbers of ancestral populations (K). Each individual is represented by a vertical bar that can be partitioned into colored fragments with length proportional to cluster contribution. K = 4 approximates the ancestral European B. taurus, African B. taurus, B. indicus and B. javanicus populations. K = 7 distinguishes between the two zebu ancestors that generated GIR and NEL, and PO exhibits contributions from both ancestral populations. See Material and Methods for breed abbreviations

Mentions: Results from the model-based clustering analysis are found in Fig. 2. When K = 4 was assumed, European B. taurus, African B. taurus, B. javanicus and B. indicus breeds were assigned to different clusters. SGT and BMA presented an average B. indicus contribution of 34 %, whereas BRM exhibited an average of 6 % of B. taurus ancestry. Interestingly, backcrossing to Ongole bulls over the course of 100 years was not capable of eliminating all B. javanicus introgression in PO cattle, which presented a mean B. javanicus ancestry of approximately 6 %. Historical hybridization with B. javanicus cattle seems to also extend to other Indonesian B. indicus populations, such as the Brebes [21] and Madura [21, 23] breeds. This is in contrast with the historical B. taurus introgression in NEL and GIR [3], which seems to have been consistently eliminated by intensive backcrossing [20, 21, 24]. This suggests that either B. javanicus haplotypes were kept by selective forces, or backcrossing in Indonesia was not as strong as in Brazil, and B. javanicus haplotypes are just drifting in PO cattle.Fig. 2


Evidence of Bos javanicus x Bos indicus hybridization and major QTLs for birth weight in Indonesian Peranakan Ongole cattle.

Hartati H, Utsunomiya YT, Sonstegard TS, Garcia JF, Jakaria J, Muladno M - BMC Genet. (2015)

Model-based clustering of cattle breeds assuming different numbers of ancestral populations (K). Each individual is represented by a vertical bar that can be partitioned into colored fragments with length proportional to cluster contribution. K = 4 approximates the ancestral European B. taurus, African B. taurus, B. indicus and B. javanicus populations. K = 7 distinguishes between the two zebu ancestors that generated GIR and NEL, and PO exhibits contributions from both ancestral populations. See Material and Methods for breed abbreviations
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4491226&req=5

Fig2: Model-based clustering of cattle breeds assuming different numbers of ancestral populations (K). Each individual is represented by a vertical bar that can be partitioned into colored fragments with length proportional to cluster contribution. K = 4 approximates the ancestral European B. taurus, African B. taurus, B. indicus and B. javanicus populations. K = 7 distinguishes between the two zebu ancestors that generated GIR and NEL, and PO exhibits contributions from both ancestral populations. See Material and Methods for breed abbreviations
Mentions: Results from the model-based clustering analysis are found in Fig. 2. When K = 4 was assumed, European B. taurus, African B. taurus, B. javanicus and B. indicus breeds were assigned to different clusters. SGT and BMA presented an average B. indicus contribution of 34 %, whereas BRM exhibited an average of 6 % of B. taurus ancestry. Interestingly, backcrossing to Ongole bulls over the course of 100 years was not capable of eliminating all B. javanicus introgression in PO cattle, which presented a mean B. javanicus ancestry of approximately 6 %. Historical hybridization with B. javanicus cattle seems to also extend to other Indonesian B. indicus populations, such as the Brebes [21] and Madura [21, 23] breeds. This is in contrast with the historical B. taurus introgression in NEL and GIR [3], which seems to have been consistently eliminated by intensive backcrossing [20, 21, 24]. This suggests that either B. javanicus haplotypes were kept by selective forces, or backcrossing in Indonesia was not as strong as in Brazil, and B. javanicus haplotypes are just drifting in PO cattle.Fig. 2

Bottom Line: We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle.Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle.This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization.

View Article: PubMed Central - PubMed

Affiliation: Beef Cattle Research Station, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jln. Pahlawan no. 2 Grati, Pasuruan, East Java, 16784, Indonesia. hartati06@yahoo.com.

ABSTRACT

Background: Peranakan Ongole (PO) is a major Indonesian Bos indicus breed that derives from animals imported from India in the late 19(th) century. Early imports were followed by hybridization with the Bos javanicus subspecies of cattle. Here, we used genomic data to partition the ancestry components of PO cattle and map loci implicated in birth weight.

Results: We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle. Only two nearly fixed B. javanicus haplotypes were identified, suggesting that most of the B. javanicus variants are segregating under drift or by the action of balancing selection. The zebu component of the PO genome was estimated to derive from at least two distinct ancestral pools. Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle.

Conclusions: This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization. Additionally, previously described loci implicated in body size in worldwide beef cattle breeds also affect birth weight in PO cattle.

No MeSH data available.