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Simple Summary: The study investigates how continuous selective breeding influenced the genetic composition and performance of the KiwiCross® composite breed, a hybrid of Holstein-Friesian and Jersey cattle known for its high milk production and quality. By examining thousands of animals, we aimed to identify specific regions in the cattle genome that contribute to enhanced productivity, such as increased milk yield and efficiency. The findings suggest that targeted breeding practices can preserve beneficial genetic traits from both parent breeds, improving performance over successive generations. Specific regions of the genome under trait selection can be traced back to specific parental breeds and highlighted for genomic improvement and selection programs. However, the study also highlights the risk of losing genetic diversity when more emphasis is placed on one parent breed over others, which could reduce the overall health and sustainability of the breed. These insights are valuable for dairy farmers and breeders seeking to optimize cattle production while maintaining long-term genetic health, offering a pathway to more sustainable and efficient agricultural practices. Composite crosses result from the mating of two or more distinct cattle breeds. Breeding performance may improve rapidly using a well-organized composite breeding system and a clear selection index. The KiwiCross® is a popular composite cross in New Zealand, combining Holstein-Friesian (high milk production) and Jersey (high milk fat). Production efficiency (PR), a key selection index, is calculated by dividing milk solids produced by mature live weight. Over decades of genetic improvement, KiwiCross® increased milk production significantly. We hypothesized that certain genomic regions from Holstein-Friesian or Jersey breeds were preserved due to artificial selection based on PR. Analysis of genomic regions using XP-EHH, hapFLK, and ROH haplotype statistics revealed selection signatures on BTA 7 and 20 in both high- and low-performance animals, with distinct regions linked to Holstein-Friesian and Jersey ancestry. Our findings suggest that selection acted on different genomic regions across generations and that preserving key ancestry-specific haplotypes is crucial for maintaining performance in composite breeds. Breeders must recognize that selection for specific traits can alter allele frequencies and lead to the loss of beneficial breed-specific haplotypes over time. [ABSTRACT FROM AUTHOR]

Indigenous chickens are an important Farm Animal Genetic Resource (FAnGR) in South Africa as they alleviate poverty and are a source of protein. Climate change and market demand for high-performing exotic breeds threaten and undermine locally adapted village chickens. The current study explored the risk status and signatures of adaptation of village-based indigenous chickens from two provinces and mapped their environmental suitability across the country. A total of 244 village chickens from rural areas of the Capricorn (n = 85) and Sekhukhune (n = 113) districts of Limpopo province; the Harry Gwala (n = 21) and uMzinyathi (n = 25) districts of KwaZulu-Natal province were genotyped using the Illumina 60K BeadChip. The conservation flock comprised Ovambo (OV; n = 10), Potchefstroom KoeKoek (PK; n = 20), and Venda (VD; n = 20). Naked Neck (NN; n = 20), New Hampshire (NH; n = 10), White Leghorn (WL; n = 10), and White Plymouth Rock (WR; n = 10) from the Agricultural Research Council Poultry Breeding Unit were used as reference populations and representative of flocks under conservation. The effective population size (Ne) in village chickens and conserved flocks ranged from 18 to 53 and 26 to 38 at 12 generations ago, respectively. PC1 and PC2 explained 5.64% of the total variation, which resulted in five clusters with the Venda, Naked Neck, and White Leghorn being separated from village chickens. The first three redundancy analysis (RDA) axes capture 46.8% of the total genetic variation used to detect significant outlier SNPs. A total of 386 outlier SNPs associated with all 10 environmental variables were detected. Using ecological niche modeling, chickens from Dipakakeng, Mgababa, and Podu villages, Limpopo, had a localized predicted suitability probability, while chickens originating from Nhlonga village, KwaZulu-Natal, had a broader distribution of predicted suitability habitats with elevation and BIO6 being important variables. The results of this study provide insight into the risk status, geographic suitability, and contributing environmental factors of indigenous chickens that can be used to influence conservation and improvement decisions. [ABSTRACT FROM AUTHOR]