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The Application of Whole Genome Sequencing (WGS) in Agricultural Breeding

Whole genome sequencing (WGS) has revolutionized the field of genetic breeding by enabling breeders to identify and select desirable genetic traits in organisms. It provides a complete genetic profile of an organism, which can be used to identify genes associated with important traits such as disease resistance, productivity, and yield. In the field of plant and animal breeding, WGS has numerous benefits that can enhance the selection of crop traits, animal population research, and evolution study. The following publications offer innovative ideas that we hope will serve as a reference for all breeder scientists’ research.

Accurate Trait Selection

WGS can help breeders to identify specific genes and genetic variations that are responsible for important crop traits such as disease resistance, yield, and drought tolerance. By identifying the specific genes that are responsible for a particular trait, breeders can use this information to select for the desired trait more accurately and efficiently. As reported by Chunhui Li et al from Chinese Academy of Agricultural Sciences, with bioinformatics assistance from H. Lu, M. Yang, and L. Huang of the Novogene Bioinformatics Institute, that by crossing two maize parental self-lines with heterotic groups, monohybrid maize self-lines with improved heterosis may be formed. In order to enable the precise genotype determination, they used WGS to re-sequence for 21 agronomic characteristics. It was observed that convergent selection traits (early flowering, shorter pollen-spat interval, etc. in both parents) were mostly associated with the breeding goal of dense and high yield while divergent selection traits (ears thickness, number of rows, etc.) might be associated with maturity and seed dehydration rate of the parent along with its hybrids. In this study, a large number of candidate genes were identified by genome-wide selection scan and association analysis to improve agronomic traits in female and male heterozygous groups (FHGs). The accumulation of favorable alleles in the parental heterozygous groups was found to be highly correlated with both convergent and divergent trait improvement. Gene editing and transgenic techniques were used to validate two modern breeding genes. The role of two modern breeding genes; ZmEMF1L1 and ZmKW10, and one divergent gene; ZmKOB1, in regulating flowering time, seed size, and hybrid advantage in maize was verified using gene editing and transgenic techniques. This research offers a sound theoretical foundation and genetic resources for the development of genome-wide selective breeding methods, selection and breeding of highly dominant hybrids, as well as genetic improvement of heterozygous populations of maize hybrids.[1]

Improved Population Research

WGS can provide a wealth of information about the genetic diversity of populations. By analyzing the entire genome of many individuals from a population, breeders can better understand the genetic variation within a population and how it is distributed. This information can be used to identify individuals that carry specific traits of interest and to design breeding programs that target specific traits. Feng-Hua Lv et al. from China Agricultural University selected 810 sheep samples from 165 populations of wild, endemic, and improved sheep breeds for high-depth resequencing. 61 million novel SNPs were identified and phylogenetic relationships were constructed between wild and domesticated sheep. It was discovered that by adapting to diverse habitats, introducing genetic changes under various production techniques, and dispersing to various regions of the world, sheep have evolved into distinctive breeds. The genomic variation, adaptive traits, and agriculturally significant traits in domesticated sheep are not entirely genetically segregated—are largely influenced by extensive variation in local and improved breeds. Domesticated sheep were also found to contain six geographically distributed genomic components. This indicates that there is a large amount of gene exchange between superior genetic populations from different continents during the breeding of differently domesticated sheep. This study made an extensive analysis about the genes associated with wool fineness traits, and for the wool traits. Four phenotypes were classified as hair, coarse-wool, medium-wool, and fine-wool. The comparison of XP-CLR, π ratio, allele frequency distribution, haplotype patterns, and sequences of different species together revealed a novel mutation in the IRF2BP2 gene. A novel mutation (chr25: T7,068,586C) in the IRF2BP2 gene was found to have a direct effect on the gene related to the variation of wool fiber diameter. Besides offering germplasm resources for a significant number of genetic variations, this study reflects researchers’ understanding of genomic variations in sheep.[2]

Understanding Plant Evolution

WGS can also help researchers to better understand the evolutionary history of crops. By comparing the genomes of different crops and their wild relatives, researchers can learn about the genetic changes that have occurred during domestication and breeding. This information can be used to develop new breeding strategies that take advantage of the genetic diversity that exists within wild crop relatives. Garlic is a completely sterile crop having significant value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown. Ningyang Li et al. from the Chinese Academy of Agricultural Sciences released a garlic genome variation map comprising 129.4 million variations in Genome Biology, with assistance from Meng Liu et al. from the Novogene Bioinformatics Institute. Evolutionary analysis showed that two populations (CG1 and CG2) cultivated in China were domesticated from two independent routes. Association analysis with the transcriptome revealed that 15.0% and 17.5% of genes were differentially expressed in the two cultivated populations, resulting in a remodeling of their transcriptome structure. The study found differential selection for bulb traits in these two garlic species throughout domestication by genome-wide trait association analysis. The research offers a valuable resource for garlic genomic breeding as well as a comprehensive explanation of the evolutionary history of this asexually reproducing crop. [3]

In summary, the advent of WGS has unlocked new opportunities for genetic breeding by providing a complete understanding of an organism’s genome. This knowledge can be utilized to identify desirable traits and develop breeding programs that focus on improving these traits. Novogene has re-optimized the existing products, enhanced and upgraded the experimental aspects such as second-generation library building and sequencing, and also conducted technical updates in the analytical aspects such as GWAS and variety identification. In the future, Novogene will closely combine the resequencing of plants and animals with breeding analysis to provide better services for customers in the field of sequencing research and breeding.
Learn more about our services: Animal and Plant Whole Genome Sequencing – Novogene

  Applications of Animal and Plant Whole Genome Sequencing
  –   Reveals the molecular mechanism referring to breeding and speciation.
  –   Investigates the origin and evolution of species.
  –   Provides resources for accelerating genetic development.
  –   Identifies common genetic variations among populations.
  Benefits of Animal and Plant Whole Genome Sequencing
  Identify Genomic variations:
  –   Single nucleotide polymorphisms (SNPs).
  –   Structural variations (SVs).
  –   Copy number variations (CNVs).

The application and benefits of animal and plant WGS– Novogene


[1] Li C, Guan H, Jing X, et al. Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding[J]. Nature Plants, 2022(7):8.

[2] Lv F H, Cao Y H, Liu G J, et al. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression, and agronomically important loci[J]. Molecular biology and evolution, 2022, 39(2): msab353.

[3] Li N, Zhang X, Sun X, et al. Genomic insights into the evolutionary history and diversification of bulb traits in garlic[J]. Genome Biology, 2022, 23(1):1-23.