Together we innovate agrigenomics

An improved reference genome and multiple genotyping platforms for better marker-assisted breeding in oil palm

Ai-Ling Ong ^1*, Chee-Keng Teh ¹, Qi-Bin Kwong¹, Sean Mayes², David Ross Appleton^1
1Biotechnology and Breeding Department, Sime Darby Plantation R&D Centre, 43400 Serdang, Selangor, Malaysia
²School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough LE12 5RD, UK
^*Corresponding author: ong.ailing.sdtc@simedarbyplantation.com

The first production of genome-enabled commercial oil palm seeds namely, GenomeSelect^TM was developed and field planted in 2016. Throughout the journey of marker discoveries, high-density SNP genotyping arrays were initially developed and used. We found that genome-wide association study-guided genomic selection (GS) achieved higher prediction accuracy than the conventional GS method. We have also developed an ultrahigh-density genetic map using 27,890 linked SNP markers representing 16 pseudo-chromosomes for a commercial population. The genetic map then coupled with the latest sequencing methods, enabling construction of an improved oil palm reference genome. This important milestone is to further enhance higher GS predictive ability and mapping precision of genes. In terms of marker applications, about 30,000 commercial seeds per month were genotyped using KASP^TM technology from LGC, Biosearch Technologies (GS1000^TM) for the selection of high-yielding planting materials. More recently, SeqSNP targeted genotyping by sequencing technology from LGC, Biosearch Technologies was also evaluated, the platform resulted in more than 95% genotypic reproducibility, which can be considered for future discovery and application purposes.

Dr. Zeng Qingdong is from Northwest Agriculture and Forestry University. He engaged in the research of wheat disease resistance genes (QTL) mapping, map based cloning, and genome sequencing. Moreover, he participated in providing the medial material and parent selection for improvement of breeding for disease resistance based on marker assisted selection.

In this workshop, he will be talking on the following: (1) Rapid identification of stripe rust resistance genes (QTL) in hexaploid wheat by high-throughput sequencing (genotyping) of pooled extremes or genome-wide association study; development of kompetitive allele specific PCR (KASP^TM,, LGC, Biosearch Technologies) markers for improvement of breeding for disease resistance by marker assisted selection
(2) Map based cloning of disease resistance gene such as wheat stripe rust gene Yr26.
(3) Carried out the genome sequencing of complex genome (underway: common wheat cv. Chinese spring chromosome short arm 2DS and dikaryon fungi)

BHQplex(^TM) CoPrimers(^TM) - Redefining Multiplex PCR

Marker assisted selection (MAS) and Marker assisted backcrossing (MABC) are critical applications in breeding pipelines that are common across species being bred. Independent of species being tested, these critical breeding applications rely on technology platforms that are fast, accurate, and affordable. In most cases, sample demand outpaces budget availability - and even with flat, or sometimes declining, budgets, researchers and lab directors are still being asked to deliver more. Multiplex PCR is a viable option for accelerating data generation, maintaining data quality, and delivering more data per R&D dollar spent. BHQplex CoPrimers, the newest PCR technology in LGC, Biosearch Technologies’ portfolio, overcomes a critical challenge of traditional multiplex PCR by enabling assay interchangeability - a capability that no other multiplex PCR technology can deliver. Now multiplex PCR can move beyond a set panel of targets run over many samples, and can be broadly deployed as a cost-saving technology - allowing labs to meet the demand to do more with less.

SeqSNP targeted GBS, an alternative to array genotyping in routine breeding programs

Dusty Vyas, Farah Aladin, Wolfgang Zimmerman, Samuel Arvidsson, Joris Parmentier. LGC; Queens Road, Teddington, Middlesex, TW11 0LY, UK.

Comprehensive assessment of complex traits and genome wide association studies (GWAS) has up to recently only been possible using fixed arrays. SeqSNP, a refined targeted genotyping by sequencing (targeted GBS) technology has been developed by LGC, Biosearch Technologies. SeqSNP not only provides flexibility in single nucleotide polymorphism (SNP) sequence selection, but also scalability in sample numbers which can be restrictive on fixed arrays. Independently analysed data is presented here, which not only substantiates that the SeqSNP service delivers genotyping data with high concordance to array genotyping, but it also surpasses other sequence based genotyping options in de novo SNP discovery (5,733 in this study) and the analysis of multi-allelic target SNP sequences.

GWAS requires larger numbers of associated markers to accurately estimate breeding values as part of a genomic selection (GS) breeding strategy. The high density of markers (>10K unique data points per sample) are required to be evenly distributed throughout a genome, (to increase genotypic resolution and phenotypic association to complex traits), thus improving prediction accuracy for training populations to be used for any GS breeding program. Of the 500 SNP sequences selected by an independent third party, 99% of SNPs were successfully genotyped using SeqSNP, compared to 90% on the fixed array. The impact of increased accuracy allows cost efficiency and increased confidence in selections made using targeted GBS. SeqSNP is the next stage in sequence based genotyping as services or bespoke kits for all breeding communities.