# Comprehensive Identification of the Bovine KLF Gene Family and Its Functional Regulation in Muscle Development: Insights from Single-Nuclei Transcriptomics

## TL;DR

This study identifies 14 KLF genes in cattle and finds that specific KLF genes, like KLF6, KLF9, KLF10, and KLF12, are important for muscle development differences between beef and dairy cattle breeds.

## Contribution

The study provides the first comprehensive characterization of the KLF gene family in cattle and identifies breed-specific regulatory genes for muscle development.

## Key findings

- 14 KLF genes were identified in the cattle genome through phylogenomic analysis.
- KLF6, KLF9, KLF10, and KLF12 were found to be key drivers of transcriptional differences between beef and dairy cattle breeds.
- Single-nuclei RNA sequencing revealed cell-type-specific expression patterns of KLF genes in muscle tissue.

## Abstract

Beef production is important for global food security. Understanding the genetic factors that control muscle growth and meat quality in cattle is key to improving breeding strategies. This study focused on a family of genes called KLF transcription factors, which are known to be master regulators of growth and metabolism. We systematically identified 14 KLF genes in the cattle genome. Using advanced single-nuclei RNA sequencing technology, we mapped the activity of these genes across different cell types (such as muscle fibers, fat cells, and immune cells) in the muscle tissue of two cattle breeds: Angus (beef breed) and Holstein (dairy breed). We discovered that the activity of these KLF genes varies greatly between cell types and between breeds. Using a machine learning approach, we identified KLF6, KLF9, KLF10, and KLF12 as key genes that may drive the differences in muscle development between the two breeds. Our findings provide valuable genetic targets for future breeding programs aimed at enhancing beef quality and yield.

The Krüppel-like factor (KLF) family of transcription regulators plays pivotal roles in adipogenesis, myogenesis, and metabolism. While comprehensively studied in humans and mice, its characterization in cattle remains limited, especially within the skeletal muscle niche. This study aimed to systematically characterize the KLF family in Bos taurus and elucidate its role in breed-specific muscular development. We employed an integrated approach of comparative genomics and single-nucleus RNA sequencing (snRNA-seq) on longissimus dorsi muscle from Angus (ANG, beef breed) and Holstein (HST, dairy breed) cattle. Phylogenomic analysis identified 14 KLF genes, revealing evolutionary conservation and potential functional divergence. snRNA-seq delineated 11 distinct cell populations and uncovered cell-type-specific expression patterns of KLFs. Further machine learning based analysis pinpointed KLF6, KLF9, KLF10, and KLF12 as key global drivers of transcriptional differences between breeds, while KLF6 was identified as a major cell-type-specific contributor in lymphatic endothelial cells. Our work provides a foundational resource for understanding the KLF family in cattle and identifies promising candidate genes for improving meat production traits through molecular breeding.