Moving towards haplotype-based analysis to accelerate genetic gains in both crops and livestock

Genomics-assisted breeding (GAB) offers a powerful tool to accelerate the improvement of crops and livestock, enabling more efficient, precise, and sustainable agricultural practices. This is made possible by the availability of cost-effective genotyping technologies and phenotyping platforms which enable precise dissection of the genome architecture of plant traits, facilitating data-driven selection in breeding programs. Different GAB approaches such as marker-assisted background selection (MABC), marker-assisted selection (MAS), Genomic Selection (GS), and marker-assisted recurrent selection (MARS) have been widely used to develop tailor-made crops. However, in most GAB approaches, high-density single nucleotide polymorphism (SNP) markers are often used and treated as individual variables in analysis tools.

Yet, we know that genetic inheritance is driven by segments of closely linked nucleotides known as ‘haplotypes’. Incorporating a true genetic inheritance step through haplotypes could potentially provide a more complete picture of the genetics contributing to trait phenotypic variations. Thus, haplotypes hold great potential for increasing the efficiency and precision of GAB approaches and fast-tracking breeding.

Many key plant traits are polygenic in nature, controlled by several genes. By using haplotype blocks, rather than focusing on locus-specific markers, we can better capture genetic diversity, the complexity of linked loci, and interactions between genes that contribute to trait expression. Incorporating haplotype information in the different GAB approaches could potentially improve precision in the selection and accuracy of genomic prediction. The advent of third-generation sequencing technologies, coupled with bioinformatics tools, is facilitating the rapid and accurate construction of haplotypes. Haplotype-based breeding has the potential to identify and accelerate integration of superior allelic combinations into future cultivars for long-term food security and sustainable productivity.

Considering significant advancements and common challenges across plant and animal agriculture—including genetic improvement, disease resistance, and climate adaptation—we welcome submissions focused on both crop and livestock improvement. Broadening the discussion to include both sectors will foster a more holistic understanding of innovation and sustainability in agriculture. We particularly encourage contributions that explore genomics-assisted breeding (GAB) methodologies, innovations, and the challenges encountered in either or both domains

The research topic welcomes submission of original research papers, review papers, and methods including (but not limited to) research on the following subjects:
• Haplotypes: Progress and Perspectives
• Haplotype estimation/phasing: New methods/tools/models for identifying haplotype blocks
• Haplotype-based phylogenetic analysis and population genomics
• Haplotype-phenotype trait association analysis to identify superior haplotypes
• Applications of haplotypes in genomic selection and other GAB approaches
• Challenges associated especially in the context of complex crop and livestock genomes