The objectives of this study were two-fold. Firstly, to estimate the likely correlated responses in milk urea nitrogen (MUN) concentration, lactation yields of milk (MY), fat (FY) and crude protein (CPY) and mature cow liveweight (LWT) under three selection scenarios which varied in relative emphasis for MUN; 0% relative emphasis (MUN0%: equivalent to current New Zealand breeding worth index), and sign of the economic value; 20% relative emphasis positive selection (MUN+20%), and 20% relative emphasis negative selection (MUN−20%). Secondly, to estimate for these three scenarios the likely change in urinary nitrogen (UN) excretion under pasture based grazing conditions. The predicted genetic responses per cow per year for the current index were 16.4 kg MY, 2.0 kg FY, 1.4 kg CPY, −0.4 kg LWT and −0.05 mg/dL MUN. Positive selection on MUN in the index resulted in annual responses of 23.7 kg MY, 2.0 kg FY, 1.4 kg CPY, 0.6 kg LWT and 0.10 mg/dL MUN, while negative selection on MUN in the index resulted in annual responses of 5.4 kg MY, 1.6 kg FY, 1.0 kg CPY, −1.1 kg LWT and −0.17 mg/dL MUN. The MUN−20% reduced both MUN and cow productivity, whereas the MUN+20% increased MUN, milk production and LWT per cow. Per cow dry matter intake (DMI) was increased in all three scenarios as milk production increased compared to base year, therefore stocking rate (SR) was adjusted to control pasture cover. Paradoxically, ten years of selection with SR adjusted to maintain annual feed demand under the MUN+20% actually reduced per ha UN excretion by 3.54 kg, along with increases of 63 kg MY, 26 kg FY and 16 kg CPY compared to the base year. Ten years of selection on the MUN0% index generated a greater reductions of 10.45 kg UN and 30 kg MY, and increases of 32 kg FY and 21 kg CPY per ha, whereas the MUN−20% index reduced 14.06 kg UN and 136 kg MY with increases of 32 kg FY and 18 kg CPY compared to base year. All three scenarios increased partitioning of nitrogen excreted as feces. The selection index that excluded MUN was economically beneficial in the current economic circumstances over selection indices including MUN regardless of whether selection was either for or against MUN. There was no substantial benefit from an environmental point of view from including MUN in the Breeding Worth index, because N leaching is more a function of SR rather than of individual cow UN excretion. This study demonstrates that attention needs to be paid to the whole system consequences of selection for environmental outcomes in pastoral grazing circumstances.

The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using grazing, mixed-breed, dairy cows in New Zealand. Phenotypes from 634 Holstein Friesian, Jersey or crossbred cows were obtained from two herds at Massey University. A subset of 490 of these cows was genotyped using Bovine Illumina 50K SNP-chips. Two genome-wise association approaches were used, a single-locus model fitted to data from 490 cows and a single-step Bayes C model fitted to data from all 634 cows. The single-locus analysis was performed with the Efficient Mixed-Model Association eXpedited model as implemented in the SVS package. Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10−6 were considered as putative quantitative trait loci (QTL). The Bayes C analysis was performed with the JWAS package and 1-Mb genomic windows containing SNPs that explained > 0.37% of the genetic variance were considered as putative QTL. Candidate genes within 100 kb from the identified SNPs in single-locus GWAS or the 1-Mb windows were identified using gene ontology, as implemented in the Ensembl Genome Browser. The genes detected in association with FP (MGST1, DGAT1, CEBPD, SLC52A2, GPAT4, and ACOX3) and CPP (DGAT1, CSN1S1, GOSR2, HERC6, and IGF1R) were identified as candidates. Gene ontology revealed six novel candidate genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, and ASS1) significantly associated with MU whose functions were in protein catabolism, urea cycle, ion transportation and N excretion. One novel candidate gene was identified in association with ECPU (MAP3K1) that is involved in post-transcriptional modification of proteins. The findings should be validated using a larger population of New Zealand grazing dairy cows.

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Genetic diversity of Sri Lankan goats (Capra hircus) was evaluated using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method to detect polymophism in four candidate genes (LALBA, k-CSN3, GnRHR and BMP4) in a sample of 219 goats representing three phenotypic groups. All studied loci were polymorphic, having three morphs for BMP4, LALBA and two morphs for k-CSN3 and GnRHR in the study population. A significant difference between genotypic frequencies for BMP4 and GnRHR genes was found while PIC criterion revealed an intermediate polymorphism for all analyzed phenotypic groups except for k-CSN3 and GnRHR genes. Cross-bred animals for BMP4 gene and nondescript animals for LALBA gene were comparatively more polymorphic according to the effective allele number criterion. This study provides insight into the genetic diversity of Sri Lankan goats, which can be utilized to develop single nucleotide polymorphism markers to be used in association studies, and marker assisted selection.

In the present study, genetic polymorphism in exon 4 of kappa casein (k-CSN3), exon 2-3 of alpha lactalbumin (LALBA) and exon 1 of gonadotropin releasing hormone receptor (GnRHR) genes were analyzed as candidate genes for milk production, milk quality and prolificacy aiming to provide information for future studies on genetic improvements in non-descriptive local goats in Sri Lanka. Altogether eleven, thirteen and three single nucleotide polymorphisms (SNPs) were identified in k-CSN3, LALBA and GnRHR gene fragments respectively utilizing the DNA sequencing technique in Sri Lanka. Seven polymorphic sites out of eleven in k-CSN3 gene fragment and the recorded polymorphic site in exon 3 of LALBA gene fragment were homozygous while all three polymorphic sites in GnRHR gene fragment were heterozygous. Two of the SNPs recorded in the present study are found to unique for Sri Lankan nondescript goat population at G203T and A730G in k-CSN3 and GnRHR genes respectively. The study records another two SNPs in GnRHR gene which are already known to be correlated with higher fecundity in goats (G757A and G891T). Results of the present study will be extremely important in future attempts to indicate markers to improve the milk production, composition of milk and litter size of nondescript local goats in Sri Lanka.