@article {3672,
	title = {Optimising a panel of single nucleotide polymorphisms for genomic prediction in New Zealand sheep},
	journal = {New Zealand Journal of Animal Science and Production},
	volume = {81},
	year = {2021},
	month = {01/2022},
	pages = {117-121},
	address = {Online},
	abstract = {A national genetic evaluation called the New Zealand Genetic Evaluation (NZGE) is undertaken weekly to support the genetic improvement of sheep via selective breeding in New Zealand (NZ). This is based on single step genomic best linear unbiased predictions (ssGBLUP), which allows animals that have genotypes and pedigree, or just pedigree, to be included in the same analysis (or evaluation). In theory, an optimal strategy is that the density and quality of SNPs used should be high enough to track all the haplotypes segregating in the population to be evaluated. Since genomic predictions have been used in NZ sheep, the content of the SNP panel used has decreased to a panel of 41K; despite that there are new SNP panels with more content available.. The effect of using this additional content and additional SNPs from an Ovine 600K chip was investigated using the trait fleece weight at 12-months. We found that a high density panel provided more accurate predictions. However, a SNP panel based on the 50K SNPs plus a relatively small subset of additional SNPs (e.g. from the 600K Chip), were as predictive as using the high density panel. We conclude that increased SNP density, beyond the 41K selected from the Ovine 50K SNP, chip will improve prediction accuracy. Our results suggest that the inclusion of SNPs from putative quantitative trait loci (QTL) may also improve prediction accuracy. However, further analyses will be helpful to distinguish the relative benefit to accuracy of increased SNP density across the genome and/or inclusion of SNPs associated with QTL.


Keywords: sheep, genetics, genomics, breeding, ssGBLUP, genomic prediction},
	issn = {1176-5283},
	author = {Lee AM and Dodds KG and Newman S-AN and Campbell D and Clarke SM}
}
@article {3672,
	title = {Genetic parameters of GreenshellTM mussel traits under two harvest seasons},
	journal = {New Zealand Journal of Animal Science and Production},
	volume = {78},
	year = {2018},
	month = {07/2018},
	pages = {66-70},
	address = {Lincoln},
	abstract = {Greenshell{\texttrademark} mussels (GSM) are a mollusc endemic to New Zealand and are of economic importance to the New Zealand
aquaculture industry. The primary focus of the GSM industry is selection for increased meat weight, however, aesthetics also
influence marketability. This study focused on pedigree-based estimation of heritabilities and genetic correlations among GSM
traits collected during two harvest seasons: standard and winter. Sizes and weights were highly heritable (0.41{\textpm}0.07 to 0.92{\textpm}0.09),
and highly genetically correlated across traits and seasons (>=0.75{\textpm}0.07). Meat cover and gonad scores (measures of visual appeal)
had lower heritabilities than did size and yield traits (0.08{\textpm}0.03-0.25{\textpm}0.05). Under standard conditions, meat cover had a high
genetic correlation with gonad condition scores (0.85{\textpm}0.04). Under winter conditions the relationship between meat cover and
gonad scores was negative (-0.52{\textpm}0.19). Substantial GxE was observed across seasons (meat cover: rg=-0.58{\textpm}0.16; gonad:
rg=0.62{\textpm}0.11). Progress made from genetic selection to increase meat yield while controlling for the size may be slow, so selecting
for traits related to visual appeal may be preferable. Given that production traits are genetically similar across harvest conditions,
selection within standard conditions is likely to improve performance in both standard and winter harvests, thereby allowing for
an extended harvest period. However, the genetic improvement of visual appeal of the mussels is likely to be influenced by target
harvest season.},
	issn = {1176-5283},
	author = {Hess AS and Dodds KG and Roberts RD and King N and Symonds J and Clarke SM}
}
@conference {3672,
	title = {BRIEF COMMUNICATION: Developing genomic tools in the New Zealand Deer Industry},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {75},
	year = {2015},
	month = {07/2015},
	pages = {91-93},
	address = {Dunedin},
	abstract = { },
	issn = {1176-5283},
	author = {Rowe SJ and Clarke SM and Van Stijn TC and Hyndman DL and Ward JF and McEwan KM and Dodds KG and McEwan JC and Newman S-AN and Asher GW}
}
@conference {3672,
	title = {BRIEF COMMUNICATION: Genetic parameters for growth, carcass and meat quality traits in New Zealand sheep},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {75},
	year = {2015},
	month = {07/2015},
	pages = {94-96},
	address = {Dunedin},
	abstract = { },
	issn = {1176-5283},
	author = {Brito LF and Miller SP and Clarke SM and Dodds KG and Bain WE and Lee MA and Pickering NK and McEwan JC}
}
@conference {3672,
	title = {Contract session: Application of genetic technologies to the New Zealand sheep industry},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {75},
	year = {2015},
	month = {07/2015},
	pages = {184-187},
	address = {Dunedin},
	abstract = { },
	issn = {1176-5283},
	author = {Jopson NB and Linscott EM and Young MJ and Dodds KG and Clarke SM and Rowe SJ and Byrne TJ and Alder GF}
}
@conference {79012,
	title = {Development of a visual scoring system for ovine pneumonia at the processing plant},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {72},
	year = {2012},
	month = {Jan},
	pages = {169-171},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {Pneumonia in sheep is a consequence of multiple infectious agents compromising the host{\textquoteright}s immune system, often with the aid of environmental factors. Chronic non-progressive pneumonia (CNP) and acute fibrinous pneumonia (AP) are the main concerns to the New Zealand sheep industry. AP occurs in sheep of all ages and is more common in older lambs during the late summer early autumn period. CNP is often seen in lambs aged between five and ten months of age. Clinical diagnosis is difficult with affected lambs showing few, if any, clinical signs of illness as reviewed by (Alley 2002). Accurate diagnosis requires examination of the lung. ... continued},
	issn = {1176-5283},
	author = {Baird HJ and Clarke SM and PL Johnson}
}
