Legacy of Draught Cattle Breeds of South India
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bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427560; this version posted January 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Title : Legacy of draught cattle breeds of South India: Insights into population 2 structure, genetic admixture and maternal origin 3 4 Authors : Vandana Manomohan1,2, Ramasamy Saravanan 2, Rudolf Pichler1, Nagarajan 5 Murali2, Karuppusamy Sivakumar2, Krovvidi Sudhakar3, Raja K 6 Nachiappan4 and Kathiravan Periasamy1,5* 7 8 Affiliations : 1Animal Production and Health Section, Joint FAO/IAEA Division of 9 Nuclear Techniques in Food and Agriculture, International Atomic Energy 10 Agency, Vienna, Austria 11 2Veterinary College and Research Institute, Namakkal, Tamil Nadu 12 Veterinary and Animal Sciences University, Chennai, India; 13 3NTR College of Veterinary Science, Gannavaram, Sri Venkateswara 14 Veterinary University, Tirupati, Andhra Pradesh, India; 15 4National Bureau of Animal Genetic Resources, Karnal, Haryana, India; 16 5Animal Genetics Resources Branch, Animal Production and Health 17 Division, Food and Agriculture Organization of the United Nations, Rome, 18 Italy. 19 20 Corresponding: Kathiravan Periasamy 21 author 22 23 24 Address : Animal Production and Health Laboratory, Joint FAO/IAEA Division of 25 Nuclear Techniques in Food and Agriculture, International Atomic Energy 26 Agency, Seibersdorf, Vienna, Austria 27 28 29 Email : [email protected]; [email protected] 30 31 32 Telephone : 00431260027328 33 34 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427560; this version posted January 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 35 Legacy of draught cattle breeds of South India: Insights into population structure, 36 genetic admixture and maternal origin 37 38 Vandana Manomohan1,2, Ramasamy Saravanan2, Rudolf Pichler1, Nagarajan Murali2, 39 Karuppusamy Sivakumar2, Krovvidi Sudhakar3, Raja K Nachiappan4 40 and Kathiravan Periasamy1,5* 41 1Animal Production and Health Section, Joint FAO/IAEA Division, International Atomic 42 Energy Agency, Vienna, Austria; 2Veterinary College and Research Institute, Namakkal, 43 Tamil Nadu Veterinary and Animal Sciences University, Chennai, India; 3NTR College of 44 Veterinary Science, Gannavaram, Sri Venkateswara Veterinary University, Tirupati, Andhra 45 Pradesh, India; 4National Bureau of Animal Genetic Resources, Karnal, Haryana, India; 46 5Animal Genetics Resources Branch, Animal Production and Health Division, Food and 47 Agriculture Organization of the United Nations, Rome, Italy. 48 *Corresponding author email: [email protected]; [email protected] 49 50 51 ABSTRACT 52 The present study is the first comprehensive report on diversity, population structure, genetic 53 admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The 54 diversity of South Indian cattle was moderately higher. A significantly strong negative 55 correlation coefficient of -0.674 (P<0.05) was observed between the effective population size 56 of different breeds and their estimated FIS. The phylogeny and genetic structure analysis 57 revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu 58 breeds. The results showed the influence of Hallikar breed in the development of most Mysore 59 type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis 60 was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey 61 and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture 62 (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two 63 major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former 64 being predominant than the later. The pairwise differences among the I2 haplotypes of South 2 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427560; this version posted January 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 65 Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results 66 indicated the need for additional sampling and comprehensive analysis of mtDNA control 67 region variations to unravel the probable location of origin and domestication of I2 zebu 68 lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of 69 endangerment due to small effective population size and high rate of inbreeding (ii) lack of 70 sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in 71 zebu cattle. Availability of purebred semen for artificial insemination, incorporation of 72 genomic/molecular information to identify purebred animals and increased awareness among 73 farmers will help to maintain breed purity, conserve and improve these important draught cattle 74 germplasms of South India. 75 76 Key words: Zebu, diversity, inbreeding, genetic relationship, taurine introgression, 77 haplogroup, mismatch distribution, domestication 78 79 1. INTRODUCTION 80 Ever since domestication, animals have been used as an important source of draught power for 81 agricultural production. Among them, cattle have been used for a variety of farm operations 82 like ploughing, carting, tilling, sowing, weeding, water lifting, threshing, oil extraction, 83 sugarcane crushing and transport. Over time, with increasing mechanization of agriculture, the 84 use of draught cattle in farm operations reduced significantly and became negligible in 85 advanced economies. However, in developing countries, particularly in small holder 86 production systems and in hilly and mountainous regions, agricultural production still relies on 87 draught animal power (Zhou et al. 2018). For example, 55% of the smallholder farmers in 88 Swaziland rely on draft animal power for land cultivation, and more than 88% of draft animals 89 found on the Swazi National Land are cattle (Kienzle et al. 2013). In India, the significance of 90 draught animal power has reduced greatly in the last few decades with its share in total farm 91 power availability declining from about 78% in 1960-61 to 7% in 2013-2014 (Singh et al. 2014) 3 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427560; this version posted January 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 92 and expected to further reduce to around 5% by 2020 (Natarajan et al. 2016). Over the years, 93 the annual use of draught animals declined from about 1200-1800 hours to 300-500 hours per 94 pair per year. Consequently, the population of draught cattle steadily decreased at a negative 95 annual compound growth rate of about -0.8%, resulting in significant decline of purebred native 96 breeds. 97 India is home to the largest cattle population (13.1 % of world’s cattle population) in the world 98 which constitutes 37.3 % of its total livestock. As per the 19th livestock census, India has 190.9 99 million cattle, out of which 151 million is indigenous cattle. The diversity of Indian cattle is 100 represented by 60 local breeds, eight regional transboundary breeds and seven international 101 transboundary breeds (FAO, 2015). Of these, 41 have been registered by National Bureau of 102 Animal Genetic Resources, the nodal agency for the registration of livestock breeds in India. 103 The Indian Zebu cattle (Bos indicus) breeds have been classified into three major groups: dairy 104 type, draught type and dual-purpose cattle. The dairy type and dual-purpose cattle breeds are 105 predominantly distributed in North and North-Western India, while most indigenous draught 106 type cattle breeds are located in Southern and Eastern India. Apart from rapid mechanization 107 of agriculture in South India, the increasing cost of maintaining draught type cattle forced the 108 farmers to replace these animals with crossbred cattle that fetched better returns from the sale 109 of milk to dairy cooperatives. During late 1980s and early 1990s, the draught cattle breeds 110 started losing their economic relevance and the farmers increasingly resorted to crossbreeding 111 with commercial taurine cattle like Jersey, Holstein-Friesian and Brown Swiss. Such crossbred 112 cows approximately yielded more than double the milk as that of indigenous draught breeds. 113 Combined with farmers’ preference for crossbreds, the relatively easy access to breeding 114 services (through state animal husbandry departments, state cooperatives and private 115 inseminators, etc.) and availability of better infrastructure for artificial insemination and 116 veterinary care, the proportion of crossbred cattle among the breedable females became much 4 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427560; this version posted January