Sequencing technology is playing an increasingly important role in agriculture, spanning crops, livestock and poultry, aquatic organisms, and beyond. In recent years, significant advances have been made in animal husbandry research and crop molecular breeding. Driven by high-throughput sequencing, a range of key technologies has emerged to support genome map construction, gene discovery, and molecular breeding, ultimately strengthening the competitiveness of the agricultural industry.
In agricultural genomics, several sequencing approaches are commonly applied.
De novo sequencing
De novo sequencing is used to obtain complete genome sequence information for a species. It involves constructing different types of DNA libraries, followed by sequencing, genome assembly, and annotation using bioinformatics methods.
In a recent study published in iScience titled “The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis”, researchers from Xi’an Botanical Garden of Shaanxi Province, China, reported the first chromosome-level genome of Toxicodendron vernicifluum.
The lacquer tree (Toxicodendron vernicifluum) is an economically, industrially, and medicinally important species. However, limited genetic information has long restricted its research and utilisation. Using integrated genomic, transcriptomic, and metabolomic analyses, researchers identified candidate genes involved in urushiol and lignin biosynthesis. The availability of high-quality genomic data provides a valuable foundation for studying urushiol biosynthesis and supports future molecular breeding and genetic engineering of lacquer trees.
During the study, researchers generated 130.8 Gb of short-read data and 106.28 Gb of Oxford Nanopore long-read data using DNBSEQ™ and ONT platforms, respectively. After quality control, 124.4 Gb of high-quality DNBSEQ™ clean reads and 105.28 Gb of ONT reads were retained for analysis.
Genome-wide analysis identified 79 orthologous genes, including 33 TvPKS genes associated with urushiol biosynthesis. Based on co-expression profiles and homologous structures, the researchers reconstructed the core urushiol biosynthesis pathway at the whole-genome level.
The DNBSEQ-G400* sequencing platform supported genome assembly by generating high-quality short reads for error correction of long reads, as well as Hi-C and RNA-seq data for chromosome-level assembly.
QTL mapping
Many important agronomic traits, including yield, quality, and stress resistance, are quantitative traits. With continuous improvements in molecular markers, mapping populations, and statistical analysis methods, quantitative trait locus (QTL) mapping has become an effective approach for dissecting the genetic basis of complex traits. Increasing numbers of candidate genes within QTL intervals have now been identified and cloned in crops such as tomato, rice, and wheat.
In a study published in G3: Genes, Genomes, Genetics titled “Mapping of a major QTL controlling plant height using a high-density genetic map and QTL-seq methods based on whole-genome sequencing in Brassica napus”, researchers from the Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences investigated the genetic determinants of plant height.
Plant height is a key architectural trait that directly influences seed yield in oilseed rape. Traditional QTL mapping approaches, which rely on segregating populations derived from two inbred parental lines, are often labour-intensive, time-consuming, and costly. In recent years, combining QTL-seq with traditional QTL mapping has become an effective strategy for identifying and validating QTLs in crops.
In this study, MGI’s DNBSEQ-G400* sequencing platform was used for QTL analysis and transcriptome sequencing across 200 rapeseed F2 individuals. As a result, a major QTL controlling plant height was successfully identified on chromosome 10.
Whole-genome sequencing (WGS)
Whole-genome sequencing (WGS) enables comprehensive analysis of entire genomes and is widely used to identify genetic variations associated with important traits in animals and plants. By accelerating gene discovery, WGS helps shorten the experimental cycle of molecular breeding and is now applied across a wide range of agriculturally important species.
Researchers from the National Academy of Agricultural Science in Korea reported the “Whole-genome sequences of 37 breeding line Bombyx mori strains and their phenotypes established since the 1960s”. The study provided whole-genome sequences alongside phenotypic descriptions and images, offering valuable resources for understanding the genetic basis of economically important traits in silkworm breeding lines.
Library preparation and sequencing were completed using MGI’s DNBSEQ-G400* platform and the MGIEasy DNA Library Prep Kit.
Low-coverage whole-genome sequencing (lcWGS)
Low-coverage whole-genome sequencing (lcWGS) has emerged as a cost-effective approach for population genomics in both model and non-model species.
In the study “Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy”, researchers from China Agricultural University and South China Agricultural University developed a highly accurate, cost- and time-efficient lcWGS method to generate high-density SNP markers in a large Duroc pig population.
By analysing 21 economically important traits in commercial pig herds, the researchers conducted high-resolution genome-wide association and fine-mapping analyses. The results demonstrated that artificial selection plays a major role in shaping the genetic architecture of agricultural animals, particularly for loci associated with economically important traits, confirming the value of lcWGS for breeding applications.
Tn5 library construction and sequencing were performed on DNBSEQ™ technology-based platforms, including DNBSEQ-G400*. DNBSEQ™ technology improved genotyping accuracy at low sequencing depths, while MGI’s automated database construction workflow reduced experimental time and minimised manual errors, meeting the efficiency demands of modern molecular breeding.
From developing markers for economically important traits to advancing multi-omics research and safeguarding the health of crops and livestock, MGI delivers end-to-end sequencing solutions across diverse agricultural applications, supporting the sustainable development of global agriculture.
