Abstract

Background

   The distinctive geography and climate of Gansu Province have given rise
   to three indigenous cattle breeds—Zaosheng, Anxi, and Yangba. Renowned
   for their superior meat quality and remarkable adaptability, these
   breeds are crucial for maintaining genetic diversity. However, they are
   under threat from intensive farming practices, environmental
   degradation, and genetic drift, which could lead to an irreversible
   loss of genetic resources. Thanks to natural and artificial selection,
   these breeds possess genetic markers that enhance their adaptation to
   extreme environments and improve key economic traits. By integrating
   comprehensive genome data from multiple breeds, this study aims to
   analyze population genetics, detect composite selection signals, and
   perform functional enrichment to uncover the mechanisms behind genetic
   differentiation and adaptive evolution. This research is pivotal for
   developing resilient breeds and ensuring sustainable resource
   management.

Results

   The genetic background of local cattle breeds in Gansu shows a mix
   between indicine cattle (Bos indicus) and taurine cattle (Bos taurus),
   with geographical differentiation: Yangba cattle in the southeast
   mainly exhibit indicine ancestry (54.43%), while Anxi and Zaosheng
   cattle in the northwest show a predominance of taurine ancestry (86.51%
   and 74.81%, respectively). This divergence is closely related to
   historical ethnic migrations, geographic barriers, and gene flow along
   the Silk Road. Selection signal analysis has revealed specific
   adaptation mechanisms in different populations: Yangba cattle exhibit
   strong selection signals in the T-cell receptor pathway (FYN, FYB1) and
   skeletal development genes (SOX6), which may be related to their
   adaptation to hot and humid environments and mountainous terrain; Anxi
   cattle show adaptive evolution in nitrogen metabolism (CA8, CA10) and
   adherens junction pathways (CTNNA2), possibly reflecting the genetic
   basis for their adaptation to arid conditions; Zaosheng cattle display
   strong selection signals in muscle development (LARGE1, SGCZ) and
   immune regulation genes (SLAMF family), likely associated with enhanced
   meat production performance and increased pathogen resistance driven by
   artificial breeding.

Conclusion

   This study explores the drivers of genetic diversity and adaptive
   evolution in Gansu’s native cattle breeds, emphasizing the impact of
   geography and human activity on genetic divergence. It provides a
   theoretical basis for conserving breed resources, identifying
   functional genes, and developing breeding strategies.

Supplementary Information

   The online version contains supplementary material available at
   10.1186/s12864-025-11753-0.

   Keywords: Gansu local breeds, Population genetics, Genetic evolution,
   Whole-genome re-sequencing

Introduction

   China is one of the most diverse countries in the world in terms of
   cattle breeds, hosting numerous indigenous cattle populations with
   unique production performance and adaptive traits [[38]1–[39]4]. These
   local breeds not only play a crucial role in livestock production but
   also represent valuable genetic resources for ecosystem conservation
   and sustainable utilization [[40]5]. As an important province in
   northwest China, Gansu Province features complex and diverse topography
   and significantly varied climatic conditions, which have given rise to
   several locally adapted cattle breeds with distinctive characteristics,
   such as Zaosheng cattle, Anxi cattle, and Yangba cattle (Fig. [41]1).
   These populations exhibit notable differences in body conformation,
   growth performance, and production purposes. Among them, Zaosheng
   cattle are recognized as an elite subgroup of Qinchuan cattle. They are
   characterized by a strong, compact build, thick bones, and
   well-developed musculature, making them the largest among Gansu’s local
   cattle breeds. Known for their high meat quality and carcass yield,
   they are considered a premium beef breed [[42]6]. Anxi cattle are a
   superior local population derived from Mongolian cattle. Despite their
   small body size and relatively slow growth rate, they demonstrate
   strong adaptability to arid and extreme environmental conditions,
   making them an essential livestock resource in grassland and desert
   regions [[43]7]. Yangba cattle are also small in size, with a compact
   and robust body structure. Their agility and excellent hill-climbing
   ability make them well-suited for rearing in mountainous and forested
   areas. Additionally, they are known for their tolerance to coarse feed,
   strong disease resistance, and docile temperament. These indigenous
   breeds not only constitute a vital component of animal husbandry in
   Gansu Province but also reflect the rich genetic diversity of cattle
   breeds across China.

Fig. 1.

   [44]Fig. 1
   [45]Open in a new tab

   Map of the distribution of major cattle populations in Gansu Province

   The intensive development of modern animal husbandry has significantly
   boosted production efficiency but also led to dual challenges of
   production goal singularity and genetic resource loss [[46]8].
   Globally, local livestock breeds are gradually being replaced by
   high-yield breeds in commercial farming systems due to relatively lower
   productivity and longer economic return cycles. Additionally,
   environmental degradation, habitat reduction, and the introduction of
   foreign breeds have led to a sharp decline in the population numbers of
   some local cattle breeds [[47]9]. For instance, in Gansu Province, the
   populations of breeds like Anxi Cattle and Yangba Cattle have
   drastically declined, with some endangered breeds facing the risk of
   permanent genetic resource loss. As products of long-term natural
   selection and artificial domestication, these local breeds may possess
   critical genetic markers for adaptation to extreme environments such as
   coldness and drought within their genomes [[48]10–[49]12]. These
   genetic traits, often diluted in existing commercial breeds through
   targeted breeding, hold irreplaceable potential value in addressing new
   diseases or climate change challenges. This trend not only threatens
   the genetic diversity reserves of regional animal husbandry but could
   also lead to irreversible loss of gene resources carrying special
   genetic traits (such as environmental adaptability, disease resistance,
   coarse feed tolerance), posing a potential threat to meeting future
   climate change and epidemic challenges [[50]13, [51]14]. Such losses
   pose a threat not only to the development of animal husbandry but also
   bring immeasurable impacts on the protection and sustainable use of
   global genetic resources. Therefore, protecting and utilizing these
   local cattle breeds’ genetic resources is not only vital for
   maintaining biodiversity but also represents a significant investment
   in the future development of animal husbandry.

   Breakthroughs in genomics technology have laid an important foundation
   for the systematic protection and innovative utilization of livestock
   genetic resources. Population genetics studies based on whole-genome
   sequencing (WGS) can systematically analyze the phylogenetic
   relationships between breeds, origins and evolutionary processes, and
   selection signal regions related to adaptive traits [[52]15, [53]16].
   In recent years, by integrating forward selection signal detection with
   functional genomics analysis, researchers have successfully revealed
   the molecular mechanisms of key economic traits in various local cattle
   breeds: Xu et al. [[54]17] screened core genes related to disease
   resistance immunity, such as CD48 and PTF1A, in Kazakh Cattle through
   selection sweep analysis, revealing potential resistance mechanisms
   against extreme environments; Lyu et al. [[55]18] identified heat
   tolerance regulatory genes such as EIF2AK4 and LEF1 in southern cattle
   breeds through combined CLR, IHS, Fst, and XP-EHH analyses, elucidating
   molecular adaptation pathways for coping with high-temperature stress;
   Jin et al. [[56]19] located key genes associated with milk production
   traits, such as PGR and SLC45A1, in Dengchuan Cattle using multi-method
   strategies including θπ and CLR, providing new evidence for mining
   genetic markers of milk quality characteristics in plateau cattle
   breeds. These research achievements highlight the significant role of
   multidimensional genomic analysis in deciphering livestock adaptive
   evolution and functional gene discovery. Focusing on Gansu’s local
   cattle germplasm resources, Zaosheng Cattle, Anxi Cattle, and Yangba
   Cattle have developed unique production capabilities and resilience
   traits under long-term natural and artificial selection. However, their
   genetic evolutionary paths, adaptive molecular mechanisms, and genetic
   bases of distinctive traits remain to be systematically analyzed.
   Therefore, this study integrates resequencing data from three major
   local cattle breeds in Gansu (Zaosheng Cattle, Anxi Cattle, Yangba
   Cattle) and representative breeds both domestically and
   internationally, conducting research at the whole-genome level: (1)
   elucidating breed origins and evolutionary relationships through
   phylogenetic and population structure analyses; (2) identifying genome
   regions related to beef performance and environmental adaptability
   through composite selection signal detection (Fst, XP-CLR, θπ, etc.);
   (3) analyzing the genetic basis of important traits combining
   functional genomics approaches. In summary, the study of genomic
   selection characteristics of local cattle breeds in Gansu not only aids
   in the protection and utilization of these valuable genetic resources
   but also provides important theoretical references for cultivating