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Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits.

ABSTRACT: BACKGROUND:The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). RESULTS:The average number of ROH per animal was 55.15?±?13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (-?0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (-?0.01 to -?0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH?>?8Mb (-?0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n?=?62) and their genomic location did not largely differ within lineages. Enriched terms (p?

SUBMITTER: Peripolli E

PROVIDER: S-EPMC6142381 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits.

Peripolli Elisa E Metzger Julia J de Lemos Marcos Vinícius Antunes MVA Stafuzza Nedenia Bonvino NB Kluska Sabrina S Olivieri Bianca Ferreira BF Feitosa Fabieli Louise Braga FLB Berton Mariana Piatto MP Lopes Fernando Brito FB Munari Danísio Prado DP Lôbo Raysildo Barbosa RB Magnabosco Cláudio de Ulhoa CU Di Croce Fernando F Osterstock Jason J Denise Sue S Pereira Angélica Simone Cravo ASC Baldi Fernando F

BMC genomics 20180917 1

<h4>Background</h4>The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (F<sub>ROH</sub>), genomic relationship matrix (F<sub>GRM</sub>), and pedigree-based coefficient (F<sub>PED</sub>).<h4>Results</h4>The average number of ROH per animal was 55.15 ± 13.01 with an aver ...[more]

PMID: 30223795

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Project description:The harsh climatic conditions and paucity of potential pollinators on Southern Ocean Islands (SOIs; latitude 46°S-55°S) lead to the expectation that anemophily or self-fertilization are the dominant modes of plant sexual reproduction. However, at least some species have showy inflorescences suggesting biotic pollination or dimorphic breeding systems necessitating cross-pollination. This study investigates whether anemophily and self-compatibility are common on SOIs, whether species or genera with these traits are more widespread or frequent at higher latitudes, and whether gender dimorphy is correlated with anemophily, as might occur if reliance on pollinators was a disadvantage. Of the 321 flowering plant species in the SOI region, 34.3 % possessed floral traits consistent with anemophily. Compatibility information was located for 94 potentially self-fertilizing species, of which 92.6 % were recorded as partially or fully self-compatible. Dioecy occurred in 7.1 % of species overall and up to 10.2 % of island floras, but has not clearly arisen in situ. Gynodioecy occurred in 3.4 % of species. The frequency of anemophily and gender dimorphy did not differ between the SOI flora and southern hemisphere temperate reference floras. At the species level, gender dimorphy was positively associated with fleshy fruit, but at the genus level it was associated with occurrence in New Zealand and a reduced regional distribution. Anemophily was more prevalent in genera occurring on subantarctic islands and the proportion of species with floral traits suggestive of biotic pollination was significantly higher on climatically milder, cool temperate islands. These results support the contention that reliance on biotic pollinators has constrained the distribution of species on SOIs; however, it is also clear that the reproductive biology of few SOI species has been studied in situ and many species likely employ a mixed mating strategy combining biotic pollination with self-fertilization.

Dataset Information

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits.

Publications

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits.

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