As of June 2024, there were approximately **** million beef cattle in New Zealand, a slight decrease from the previous year, when there were around **** million beef cattle in the country. The number of beef cattle, including bulls, steers, and cows fluctuated during the measured period. Livestock farming industry in New Zealand New Zealand is well known for its superior livestock industry, especially in sheep and beef production. While the large sheep population in New Zealand has historical significance, it has declined significantly during the last ten years. The decline can be attributed to numerous factors, including the conversion of sheep farming land for alternative purposes such as urban expansion, the expansion of dairy farming, and the development of horticulture farming. Apart from sheep, there has also been a decrease in the number of lamb cattle. New Zealand’s dairy farming industry The dairy industry is vital to the country’s broader agricultural sector. New Zealand’s cows produce milk processed into various dairy products, consumed locally and internationally. Thus, the dairy industry accounts for a significant amount of New Zealand's export revenue. The environmental challenges facing dairy producers nationwide have gained increasing attention from the public and environmental organizations. The degradation of water quality and greenhouse gas emissions associated with dairy cattle production are two key issues being discussed.

The number of dairy cattle on farms in New Zealand has decreased since the beginning of the measured period, 2014, to reach approximately **** million cows as of June 2024. The milk produced from these cows is processed into a large variety of dairy products which are consumed locally and globally. Subsequently, the dairy industry makes up a large portion of New Zealand’s export income. Dairy farming Holstein-Friesian/Jersey crossbreed cows were the most common breed of dairy cow in the country. Farmers have been moving towards crossbred cows to combine the best traits from the two major dairy breeds. The Waikato and North Canterbury regions were the strongest in terms of the dairy cow distribution. While dairy farming has historically been more dominant in the North Island, herd numbers in the South Island have been increasing. Most dairy companies in the country are farmer-based cooperatives, with Fonterra leading the pack. Environmental impact The environmental challenges facing dairy farmers across the country have increasingly been highlighted by the public and environmental groups. Water quality degradation and greenhouse gas emissions due to dairy cattle farming are two of the biggest issues that have been debated. In response, the Sustainable Dairying: Water Accord was implemented in 2013 as a set of national good management practice benchmarks aimed at lifting environmental performance of dairy farms.

As of June 2024, there were approximately ***** million sheep in New Zealand, a slight decrease from the previous year in which there were around ***** million sheep in the country. The number of sheep in the country has declined over the past decade.  Sheep farming New Zealand was once known for its disproportionate number of sheep per population. However, since the 1970s, the country’s sheep population has fallen drastically. A major factor that has contributed to this decline is sheep farming land lost to other purposes such as urban sprawl, dairy farming, and horticulture farming. The number of lamb livestock has similarly seen a decline. Consumption and exports Sheep in New Zealand are bred for wool and meat, including mutton and lamb. New Zealand is a significant player in the global wool market. The country exports strong wool to leading textile manufacturers around the world. However, along with sheep numbers, wool production has decreased significantly across New Zealand. In terms of domestic meat consumption, the per capita consumption of sheep meat in New Zealand was forecast to decline into the next decade. When looking at trade, the leading country for sheep meat exports from New Zealand was China, with the United Kingdom and the United States trailing behind.

Additional file 5: Table S4. Genomic prediction accuracies for each of the five folds. validation = validation population, reference = reference validation, fold1-5 = prediction accuracy in fold 1–5, AUS_HOL = Australian Holstein, AUS_JER = Australian Jersey, NZL_HOL = New Zealand Holstein, NZL_JER = New Zealand Jersey, WC = within country reference population, MC = multi country reference population, HD = variants on the Illumina Bovine HD BeadChip, SEQ = selected sequence variants.

Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. Whilst there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Here we examine associations between genomic regions and individual FT-MIR wavenumber phenotypes within a population of 38,085 mixed-breed New Zealand dairy cattle with imputed whole-genome sequence. GWAS were conducted for each of 895 individual FT-MIR wavenumber phenotypes and three FT-MIR predicted milk composition traits, and gene annotation and mammary tissue gene expression datasets were employed to identify candidate causative genes and variants. This resulted in the identification of 38 co-locating, co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in ABO that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk.

Methods Adjusted FT-MIR spectra records for 38,085 multi-breed and crossbred New Zealand dairy cows were derived from 100,571 FT-MIR spectra records from individual milk samples collected as part of routine herd testing conducted by Livestock Improvement Corporation (LIC) in the 2017/18 season.

Imputed whole-genome sequence genotypes were generated using a stepwise imputation approach via panels of 50k and HD density.

Additional file 1: Table S1. Genomic relationships using HD and SEQ variants. Average genomic relationships within (diagonal) and between populations (below the diagonal) of genomic relationship matrices constructed using high-density (HD) or selected sequence (SEQ) variants; AUS = Australia, NZL = New Zealand.

This study aimed to develop a better understanding of the local adaptation and selection of South African, Irish, Uruguayan, and New Zealand Hereford populations in their respective environments. Before analyses, a total of 1 693 individual genotypes were received where 1 538 individuals for the four populations remained after quality control for further downstream data analyses. All individuals were genotyped using seven different arrays, as listed in Table1. Descriptive genomic diversity parameters were estimated as HE, HO, FIS, MAF, and LD using PLINK v 1.9. All populations showed a moderate level of heterozygosity with HE values ranging from 0.359 to 0.391, and HO values ranging from 0.352 to 0.388. FIS values were -0.00475 to 0.0189 with MAF values ranging from 0.24 to 0.29 and LD ranging from 0.41 to 0.70. Population structure was visualised through principal component analysis. Each population showed to have a distinct cluster with some overlap between clusters. Intra-population genomic relatedness was determined through ROH. The detectRUNS package was used in R and a consecutive runs method was applied. The Irish and New Zealand populations showed to have the lowest degree of intra-population relatedness. A high level of genetic differentiation was observed in all populations. Selection signatures and candidate genes were identified using ROH for an intra-population approach and Pairwise Wright’s FST for an inter-population approach. Most notably, intra-population candidate genes related to traits of adaptation where the KDR and KIT genes were identified. Inter-population comparisons revealed 60 candidate genes related to traits of adaptation, production, and quality. The most common trait identified was that of bovine respiratory disease susceptibility. Five candidate genes, namely ARL6, ENOPH1, PPARGC1A, SCD5, and SNCA, were found to overlap between four of the six inter-population comparisons. Production and quality-related traits aligned with the breeding objectives of each population. The candidate genes related to adaptability traits showed that each population is adapted to its environment. Overall, each population showed to be genomically diverse and adapted to its geographically separated production region.

Additional file 4: Table S3. Composition of the animals in the core set. Number of animals of each population included in the core set.

Additional file 2: Table S2. Genes located within QTL regions. chr = chromosome, start and end = start and end of QTL region in base pair (bp) on the ARS-UCD1.2 annotation, genes = list of genes located within QTL region.

Species equivalence values to an adult dairy cow that were used for analysis [29, 30].

The agriculture, forestry, and fishing industry is a major production and export industry in New Zealand. In the year ended March 2024, the gross domestic product (GDP) of this industry amounted to over **** billion New Zealand dollars.  New Zealand agriculture  Pastoral farming of sheep and cattle constitutes a large portion of the New Zealand agriculture industry. Despite continuing a declining trend, New Zealand’s sheep population exceeded ** million in 2024. Sheep meat and wool are both important agricultural commodities produced in the country. These products, along with beef and lamb, are consumed domestically as well as exported overseas. Horticulture production is also an important segment. A wide variety of fresh and processed fruit and vegetables are produced, consumed, and exported from New Zealand. The highest value of horticultural exports from New Zealand went to Asia in 2024. Changing consumption habits The consumption of beef and veal in New Zealand is projected to decrease over the next years. At the same time, global meat consumption is predicted to reduce significantly in the next 15 years, with meat replacements and alternatives filling the market. With the country’s agriculture industry dependent on its meat exports, this presents both challenges and opportunities for New Zealand agriculture.

Also shown is the mean count of LSU and cattle per farm and the standard deviation in brackets. Full results for all models are shown in the Supporting Information (S2 and S3 Tables).

Additional file 6: Table S1. Estimates (±SD) of FIS (diagonal) within the breeds and pairwise FST (above diagonal) values between the breeds.

In 2017 an outbreak of Mycoplasma bovis (M. bovis), an infectious agent of cattle, was identified in Aotearoa New Zealand. This study characterizes the genomic population structure of the outbreak in New Zealand and compares it with the known global population structure using multilocus sequence typing (MLST) and genomic analysis. The New Zealand outbreak strain was MLST genotyped as ST21. A comprehensive collection of 840 genomes from the New Zealand outbreak showed a pattern of clonal expansion when characterized by MLST, core genome MLST (cgMLST) and whole genome MLST (wgMLST). A lineage of genomes was found with no in silico identifiable pta2 locus, a housekeeping gene used in the MLST scheme. We compared a sample set of 40 New Zealand genomes to 47 genomes from other countries. This group had 79 ST21 genomes and eight genomes that were single nucleotide polymorphism (SNP) variants within the MLST loci of ST21. Two of the 47 international genomes showed signs of extensive unique recombination. Unique alleles in six genes were identified as present only in the New Zealand genomes. These novel variants were in the genes; haeIIIM encoding for cytosine-specific methyltransferase, cysC encoding for cysteinyl tRNA synthetase, era encoding for GTPase Era, metK encoding for S-adenosylmethionine synthase, parE encoding for DNA topoisomerase, and hisS encoding for histidine-tRNA ligase. This finding could be due to a population bottleneck, genetic drift, or positive selection. The same sample set of 40 New Zealand genomes were compared using MLST to 404 genomes from 15 other countries and 11 genomes without a known country. A FastBAPS analysis of 455 genomes showed a global population structure with 11 clusters. Some countries, such as Canada, Denmark and Australia contained both internally closely related genomes and some genomes that were more closely related to genomes found in other countries. Our results support the need for Whole Genome Sequencing (WGS) as well as MLST genotyping in M. bovis outbreaks. They also support the importance of understanding the national and international movement patterns of cattle and their genetic material, as possible routes of transmission, when managing the spread of M. bovis.