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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.


Multidimensional scaling analysis. When all breeds are simultaneously analyzed (a), the differences between European B. taurus (HOL), African B. taurus (NDA) and B. indicus breeds (PO, BRM, GIR and NEL) are well demonstrated. However, B. indicus breeds are poorly distinguishable due to ascertainment bias. The analysis of B. indicus breeds alone (b) resolves the relationships among BRM, GIR, NEL and PO cattle, highlighting a closer proximity between the later two. See Material and Methods for breed abbreviations
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Fig1: Multidimensional scaling analysis. When all breeds are simultaneously analyzed (a), the differences between European B. taurus (HOL), African B. taurus (NDA) and B. indicus breeds (PO, BRM, GIR and NEL) are well demonstrated. However, B. indicus breeds are poorly distinguishable due to ascertainment bias. The analysis of B. indicus breeds alone (b) resolves the relationships among BRM, GIR, NEL and PO cattle, highlighting a closer proximity between the later two. See Material and Methods for breed abbreviations

Mentions: When all breeds were analyzed simultaneously using CMDS (Fig. 1a), the first coordinate (C1, x-axis) explained the genetic differences between B. taurus, B. indicus and B. javanicus. The second coordinate (C2, y-axis) separated breeds by geographical origin, explaining genetic differences between African and non-African cattle. These findings are consistent with the previously reported clustering behavior of 50k genotypes in worldwide cattle breeds [20, 21]. As B. indicus breeds were poorly separated in comparison to the B. taurus breeds as a result of ascertainment bias [22] (see Additional file 1), the relationships among B. indicus breeds were assessed by re-running the analysis without B. taurus and B. javanicus genotypes (Fig. 1b). This analysis revealed that GIR, BRM, PO and NEL cluster as distinct populations, with PO and NEL exhibiting greater similarity. This is not unexpected, provided PO and NEL were believed to derive from the same ancestral population.Fig. 1


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)

Multidimensional scaling analysis. When all breeds are simultaneously analyzed (a), the differences between European B. taurus (HOL), African B. taurus (NDA) and B. indicus breeds (PO, BRM, GIR and NEL) are well demonstrated. However, B. indicus breeds are poorly distinguishable due to ascertainment bias. The analysis of B. indicus breeds alone (b) resolves the relationships among BRM, GIR, NEL and PO cattle, highlighting a closer proximity between the later two. 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

Fig1: Multidimensional scaling analysis. When all breeds are simultaneously analyzed (a), the differences between European B. taurus (HOL), African B. taurus (NDA) and B. indicus breeds (PO, BRM, GIR and NEL) are well demonstrated. However, B. indicus breeds are poorly distinguishable due to ascertainment bias. The analysis of B. indicus breeds alone (b) resolves the relationships among BRM, GIR, NEL and PO cattle, highlighting a closer proximity between the later two. See Material and Methods for breed abbreviations
Mentions: When all breeds were analyzed simultaneously using CMDS (Fig. 1a), the first coordinate (C1, x-axis) explained the genetic differences between B. taurus, B. indicus and B. javanicus. The second coordinate (C2, y-axis) separated breeds by geographical origin, explaining genetic differences between African and non-African cattle. These findings are consistent with the previously reported clustering behavior of 50k genotypes in worldwide cattle breeds [20, 21]. As B. indicus breeds were poorly separated in comparison to the B. taurus breeds as a result of ascertainment bias [22] (see Additional file 1), the relationships among B. indicus breeds were assessed by re-running the analysis without B. taurus and B. javanicus genotypes (Fig. 1b). This analysis revealed that GIR, BRM, PO and NEL cluster as distinct populations, with PO and NEL exhibiting greater similarity. This is not unexpected, provided PO and NEL were believed to derive from the same ancestral population.Fig. 1

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.