نشانه‌های انتخاب مرتبط با صفت تعداد بره در هر نوبت زایش میش‌های بلوچی

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانش‌آموخته دکتری، گروه علوم دامی، دانشگاه علوم کشاورزی و منابع طبیعی ساری

2 دانشیار، گروه علوم دامی، دانشگاه علوم کشاورزی و منابع طبیعی ساری

3 استاد، گروه علوم دامی، دانشگاه علوم کشاورزی و منابع طبیعی ساری

4 دانشیار، گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه اراک

چکیده

تعداد بره در هر زایش، یکی از مهم‌ترین صفات اقتصادی و تولیدمثلی در گوسفند است. در این پژوهش از داده­های 96 رأس میش نژاد بلوچی تعیین ژنوتیپ شده با استفاده از ریزآرایه‌های نانویی گوسفندی K50 برای شناسایی نواحی ژنومی مورد انتخاب مرتبط با تعداد بره در هر زایش در گوسفند استفاده شد. میش‌ها بر اساس داده­های فنوتیپی پنج شکم زایش به دو گروه مورد (دوقلوزا) و شاهد (تک­قلوزا) تقسیم شدند. برای شناسایی نشانه‌های انتخاب از آماره‌های FST و XP-EHH به ترتیب در بسته نرم‌افزاری FST و EHH و برای تجزیه هستی‌شناسی ژن‌های شناسایی شده در مناطق مورد انتخاب از پایگاه داده DAVID استفاده شد. نتایج این پژوهش منجر به شناسایی 14 ناحیه ژنومی روی کروموزوم­های 1 و 2 (دو ناحیه برای هر کدام)، 3، 7، 9، 14، 18، 22 و 23 (هر کدام یک ناحیه) و کروموزوم X (3 ناحیه) با آماره FST و 9 ناحیه ژنومی روی کروموزوم‌های 13،12،2 و 22 (یک ناحیه برای هر کدام)، 7 (سه ناحیه) و X (دو ناحیه) با آماره XP-EHH شد. برخی از ژن‌های شناسایی شده در مناطق مورد انتخاب با تعداد بره در هر زایش (ACVR1 وTGIF1 )، رشد تخمدان و فولیکول (DDX24) و باروری (FOXH1) مرتبط بودند. در مسیرهای زیستی شناسایی ‌شده، دو مسیر پاسخ دفاعی و تحرک سلولی دارای نقش مهمی در نرخ تخمک­ریزی و تعداد بره در هر زایش بودند. نتایج این مطالعه نشان داد که ژن‌های ACVR1 و TGIF1را می‌توان به ‌عنوان ژن‌های کاندید مرتبط با تعداد بره در هر زایش در برنامه‌های اصلاح نژادی گوسفند در نظر گرفت.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Selection signatures associated with the number of lambs per lambing in Baluchi ewes

نویسندگان [English]

  • M. M. Kasiriyan 1
  • M. Gholizadeh 2
  • Gh. Rahimi-Mianji 3
  • M. H. Moradi 4
1 Former Ph.D. Student, Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
2 Associate Professor, Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
3 Professor, Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
4 Associate Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
چکیده [English]

Introduction: The number of lambs per lambing is one of the most important reproductive traits in sheep. Many studies have reported that genetic mechanisms play an important role in the variation of litter size in sheep. Selection for higher litter size in sheep has led to a variation of this trait within and across different breeds. Natural and artificial selection related to adaptation and economic traits, such as litter size, results in changes at the genomic level which leads to the appearance of selection signatures. Detection of these regions provides an opportunity for a better understanding of genetic mechanisms underlying the phenotypic variation of litter size in sheep. Several tests including the linkage disequilibrium-based approach, site frequency spectrum, and population differentiation-based approach have been developed to explore the footprints of selection in the genome. This study aimed to identify selection signatures in Baluchi sheep to investigate the genes annotated in these regions as well as the biological pathways involved. For this purpose, XP-EHH and FST analyses were conducted using the genome-wide single nucleotide polymorphisms (SNPs).
Materials and methods: In this study, data from 96 Baluchi ewes genotyped using Illumina Ovine SNP50K BeadChip were used to identify genomic regions under selection associated with litter size in sheep. Phenotypic and pedigree data were collected at the Abbasabad Sheep Breeding Station. Based on records on different litters, ewes were divided into two groups: the case (two lambs per litter) and control (one lamb per litter).
Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-6. To identify the signatures of selection, two statistical methods of FST and XP-EHH were used under FST and EHH software packages, respectively. We also calculated unbiased estimates of FST. Because the results were strongly correlated with the FST results, unbiased estimates have not been reported. In our study, all the SNPs ranking above 0.1 percentile of the distribution of test statistics were selected as candidates for the signature of selection. Gene ontology analysis for identified genes was performed using DAVID online database.
Results and discussion: We used the FST and XP-EHH statistics to identify genomic regions that have been under positive selection associated with litter size in Baluchi sheep. Using FST approach, we identified 14 genomic regions on chromosomes 1 and 2 (two regions per chromosome), 3, 7, 9, 14, 18, 22, 23 (one region per chromosome), and X chromosome (three regions). Also, XP-EHH analysis identified nine genomic regions on chromosomes 2, 12, 13, and 22 (one region per chromosome), 7 (three regions), and X (two regions). Some of the genes located in identified regions under selection were associated with the number of lambs per lambing (ACVR1 and TGIF1), ovarian and follicle growth (DDX24), and fertility (FOXH1). Bone morphogenetic proteins are critical regulators of chondrogenesis during development which transduce their signals through three type I receptors namely BMPR1A, BMPR1B, and ACVR1/ALK2. TGIF1 is highly expressed in sheep ovaries suggesting that TGIF1 plays an important role in ewe reproduction. Also, TGF-β/SMAD signaling is critical in reproductive processes such as follicular activation, ovarian follicle development, and oocyte maturation. It has been evidenced that Ddx24 is highly expressed in sheep uterus affecting the development of ovaries and follicles. Foxh1 was first introduced as a transcriptional partner for Smad proteins and has been reported to play an important role in embryonic development. Results of gene ontology analysis identified two biological pathways namely defense response and cell motility which play an important role in the ovulation rate and the number of lambs per lambing. Reproductive activity and immune defenses can be mutually constraining, with increased reproductive activity limiting immune function and immune system activation leading to decreased reproductive function.
Conclusions: The results of this study identified candidate genes involved in the regulation of litter size in sheep suggesting that ACVR1 and TGIF1 genes can be considered as candidate genes related to the number of lambs per litter in sheep breeding programs to improve reproductive performance. 

کلیدواژه‌ها [English]

  • FST statistics
  • XP-EHH statistics
  • Number of lambs per lambing
  • Baluchi sheep
  • Selection signatures

مراجع

Abasi-Mashei B., Rahimi-Mianji G. H., Nejati-Jawarami A., Moradi M. H. and Son K. 2017. Genomic scan for selection signature associated with mastitis in German Holestin cow. Iranian Journal Animal Science, 48: 453-461. (In Persian).
Abdoli R., Zamani P., Mirhosseini S. Z., Ghavi Hossein-Zadeh N. and Almasi M. 2019. Genetic parameters and trends for litter size in Markhoz goats. Revista Colombiana de Ciencias Pecuarias, 32(1): 58-63.
Aldawood N., Alrezaki A., Alanazi S., Amor N., Alwasel S. and Sirotkin A. 2020. Acrylamide impairs ovarian function by promoting apoptosis and affecting reproductive hormone release, steroidogenesis and autophagy-related genes. Ecotoxicology and Environmental Safety, 197: 110595-1105599.
Al-Lawama M., Albaramki J., Altamimi M. and El-Shanti H. 2019. Congenital glucose-galactose malabsorption: A case report with a novel SLC5A1 mutation. Clinical Case Reports, 7: 51-53.
Akey J. M., Zhang G., Zhang K., Jin L. and Shriver M. D. 2002. Interrogating a high-density SNP map for signatures of natural selection. Genetics Research, 12: 1805-1814.
Bonde J. P., Flachs E. M., Rimborg S., Glazer C. H.,  Giwercman A., Ramlau-Hansen C. H. and Bräuner E. V. 2016. The epidemiologic evidence linking prenatal and postnatal exposure to endocrine disrupting chemicals with male reproductive disorders: A systematic review and meta-analysis. Human Reproduction Update, 23: 104-125.
Dolebo A. T., Khayatzadeh N., Melesse A., Wragg D., Rekik M., Haile A., Rischkowsky B., Rothschild M. and Mwacharo J. M. 2019. Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis Aries). Mammalian Genome, 11: 339-352.
Esmaeili fard S. M., Hafezian S. H., Gholizadeh M. and Abdolahi Arpanahi R. 2019. Gene set enrichment analysis using genome-wide association study to identify genes and biological pathways associated with twinning in Baluchi sheep. Animal Production Research, 8(2): 63-80. (In Persian).
Farhangfar H., Molaei M., Naeimipour H. 2007. Using the logistic regression model in estimating the phenotypic trend of twinning trait in Baluchi ewes of Abbas Abad Station, Mashhad. Modern Genetics, 3: 31-34. (In Persian).
Fariello M. I., Servin B., Tosser-Klopp G., Rupp F. and Moreno C. 2014. Selection signatures in worldwide sheep populations. International Sheep Genomics Consortium, 8: 103813-103817
Gautier M. and Vitalis R. 2012. rehh: an R package to detect footprints of‌ selection in genome-wide SNP data from haplotype structure. Bioinformatics, 8: 1176-1177.
Gholizadeh M., Rahimi-Mianji G. H. and Nejati-Javaremi A. 2015. Genomewide association study of body weight traits in Baluchi sheep. Journal of Genetics, 94: 143-146.
Jafaroghli M., Safari A., Shadparvar A. A. and N. Ghavi Hossein-Zadeh. 2019. Genetic analysis of ewe productivity traits in Baluchi sheep. Iranian Journal of Applied Animal Science, 9(4): 651-657.
Kijas J. W., Lenstra J. A., Hayes B., Boitard S., Porto Neto L. R., San Cristobal M., Servin B., McCulloch R., Whan V. and Gietzen K. 2012. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology, 2: 100-118.
Knight P. G. and Glister C. 2006. TGF-beta superfamily members and ovarian follicle development. Reproduction, 14: 191-206.
Kosgey L. S., Baker R. L., Udo H. M. J. and van Arendonk J. A. M. 2006. Success and failures of small ruminant breeding programmes in the tropics: A review. Small Ruminant Research, 61: 13-28.
La Y., liu Q., Zhang L. and Chu M. 2019. Single nucleotide polymorphisms in SLC5A1, CCNA1, and ABCC1 and the association with litter size in small-tail Han sheep. Animals, 7: 432-439.
Ma H., Fang C., Liu L., Wang Q., Aniwashi J., Sulaiman Y. and Abudilaheman K. 2019. Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing. Peer Journal, 26: 80-79. 
Manzari Z., Mehrabani-Yeganeh., Nejati-Javaremi H., Moradi M. H. and Gholizadeh M. 2019. Detecting selection signatures in three Iranian sheep breeds. Animal Genetics, 50: 298-302.
McBride D., Carré W., Sontakke S. D., Hogg C. O. and Law A. 2012. Identification of miRNAs associated with the follicular-luteal transition in the ruminant ovary. Reproduction, 144: 221-233.
Menezo Y. J., Silvestris E., Dale B. and Elder K. 2016. Oxidative stress and alterations in DNA methylation: Two sides of the same coin in reproduction. Reproduction, 33: 668-683.
Melé M., Ferreira P. G., Reverter F., DeLuca D. S., Monlong J., Sammeth M., Young T. R., Goldmann J. M., Pervouchine D. D. and Sullivan T. J. 2015. The human transcriptome across tissues and individuals. Science, 348: 660-665.
Moradi M. H., Nejati-Javaremi A., Moradi-Shahrbabak M., Dodds K. G. and McEwan J. C. 2012. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genetics, 71: 1-19.
Nosrati M., Asadollahpour-Naini H., Amiri Z. and Esmaielzadeh A. 2018. Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep. Reprouduction in Domestic Animals, 52: 358-364.
Pasandideh M., Rahimi-Mianji G., Gholizadeh M. and Fontanesi L. 2017. Detection of genomic regions affecting reproductive traits in Baluchi sheep using high density markers. Animal Production Research, 6(3): 29-41. (In Persian).
Pourtahmasebian Ahrabi M., Eskandarinasab M. P. and Zandi Baghcheh Maryam M. B. 2020. Estimation of genetic parameters and genetic trend of litter size in under selection flock of Afshari sheep. Animal Production Research, 9(2): 23-35. 
Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M. A., Bender D., Maller J., Sklar P., de Bakker P. I., Daly M. J. and Sham P. C. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81: 559-575.
Rafati M., Mohamadhashem F., Hoseini A., Hoseininasab F. and Ghari S. R. 2016. A novel ACVR1 mutation detected by whole exome sequencing in a family with an unusual skeletal dysplasia. European Journal of Medical Genetics, 59: 330–336.
Sabeti P. C., Schaffner S. F., Fry B., Lohmueller J., Varilly P., Shamovsky O., Palma A., Mikkelsen T. S., Altshuler D. and Lander E. S. 2007. Positive hatural selection in the human lineage. Science, 312: 1614-1620.
Shimizu T., Jayawardana B. C., Nishimoto H., Kaneko E., Tetsuka M. and Miyamoto A. 2006. A: Involvement of the bone morphogenetic protein/receptor system during follicle development in the bovine ovary: hormonal regulation of the expression of bone morphogenetic protein 7 (BMP-7) and its receptors (ActRII and ALK-2). Molecular and Cellular Endocrinology, 249: 78-83.
Taghizadeh K., Gholizadeh M., Moradi M. H. and Rahimi Mianji G. 2020. Investigation of copy number variation in Baluchi sheep genome using comparative analysis of PennCNV and QuantiSNP algorithms. Animal Production Research, 9(1): 29-44. (In Persian).
Wang Y., Niu Zh., Zeng Zh., Jiang Y., Jiang Y., Ding Y., Tang S., Shi H. and Ding X. 2020. Using high-density SNP array to reveal selection signatures related to prolificacy in Chinese and Kazakhstan sheep breeds. Animals, 151: 16-33.
Weir B. S and Clark-Cockerham C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 36: 1358-1370.
Xu S. S., Gao L., Xie X. L., Ren Y. L., Shen Z. Q., Wang F., Shen M., Eyþórsdóttir E., Hallsson J. H., Kiseleva T., Kantanen J. and Li M. H. 2018. Genome-Wide association analyses highlight the potential for different genetic mechanisms for litter size among sheep breeds. Frontiers in Genetics, 118: 452-459.
Yadin D., Knaus P. and Mueller T. D. 2016. Structural insights into BMP receptors: Specificity, activation and inhibition. Cytokine Growth Factor Reviews, 27: 13-34.
Yuan Z., Zhang J., Li W., Wang W., Li F. and Yue X. 2019. Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds. Animals, 11: 263-271.
Zhang Y. E. 2017. Non-Smad signaling pathways of the TGF- family. Cold Spring Harbor Perspectives in Biology, 9: 56-71.
Zhou M., Pan Z. Y., Cao X. H., Guo X. F., He X. Y., Sun Q. and Chu M. X. 2018. Single nucleotide polymorphisms in the HIRA gene affect litter size in Small Tail HanSheep. Animal Sicence, 71: 544-552.
تحقیقات تولیدات دامی
دوره 11، شماره 4
بهمن 1401
صفحه 47-60

فایل ها

هم رسانی

ارجاع به این مقاله

آمار