Program Goals and Directions
The overall goal of this program is to enhance sugar beet germplasm using conventional and molecular genetics approaches so as to advance knowledge, apply cost-effective and efficient methods to deliver high impact research results.
We are focusing on deciphering genes regulating major diseases such as; beet curly top virus (BCTV), postharvest root-rots, rhizoctonia root-rot, and beet necrotic yellow vein virus (BNYVV). Additionally, research projects on abiotic stresses, including drought and frost tolerance are part of our program. Monitoring genetic diversity of the genus Beta is an integral part of our research to broaden the genetic-base of the public germplasm.
We routinely use molecular markers such as EST-SSRs, DArT, and SNPs to increase precision and the efficiency of selection for best trait combinations. Several breeding populations and genetic mapping populations are developed and used to identify markers linked to traits and to assess the extent of linkage disequilibrium. This program cooperates with the sugar beet industry worldwide, through the sugar beet growers’ research committees, and the Beet Sugar Development Foundation (BSDF).
The public sugar beet germplasm is largely segregating populations. Rarely breeding lines or inbred parental lines are released. Thus, there is need to focus on producing highly homozygous lines for molecular genetics and inheritance studies. We released the first doubled haploid line KDH13 (PI663862) that is exceptionally resistant to beet curly top. This line has the potential to be used by seed industry as a new source of resistance for transferring curly top resistance gene(s) to varieties that lack this level of resistance. Also it has been used for the whole genome sequencing project.
Whole genome sequencing project
The public molecular genetics and genomics research in sugar beet is sparse compared to other economically important crops. This laboratory was the first to release whole genome sequence assembly of a public sugar beet breeding line (KDH13). We used Illumina HiSeq2000 next generation sequencing system. Sequencing of a standard genomic paired end and a mate-pair genomic libraries, constructed from leaf sample yielded a 68X coverage and used to generate a draft assembly (BvvSeq-1). The BvvSeq-1 assembly was released to the public in May 2013 and can be accessed here: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA176558
DNA markers development:
Single Nucleotide Polymorphism (SNP) markers:
SNP markers can be valuable for genetic studies and germplasm enhancement. To develop a large set of SNP to the scientific communities we aligned the assembly (BvvSeq-1) to the RefBeet-0.9 http://bvseq.molgen.mpg.de/Genome/start.genome.shtml. assembly. This is the first outcome of the whole genome sequencing. We selected a thousand polymorphic SNPs between KDH13 and KWS2320 based on the depth of sequencing (coverage) and variation in the flanking regions. We used the Fluidigm® SNPtype assay coupled to the IFC and EP1 reader systems. This platform offers a flexible small scale genotyping system available in the following chip formats: 24X192, 48X48, and 96X96. We deployed the 96X96 format that allows for genotyping 96 individuals using 96 SNP markers to generate 9,216 data points. These markers and other genomic resources will be used for characterization of germplasm. The table of SNP flanking sequence and amplification primers can be accessed at http://www.ars.usda.gov/sp2UserFiles/person/40864/SNP-NWISRL-USDA-Kimberly.xlsx.
We used SSRIT software and a modified version of it to identify SSRs in the public Expressed Sequence Tags (ESTs) database of sugar beet in the NCBI; http://www.ncbi.nlm.nih.gov/nuccore/?term=sugar+beet
A new set of imperfect EST-SSRs is developed in addition to perfect SSRs:
DArT markers for sugar beet
We developed the first DArT marker-system for sugar beet. It is a high-throughput and cost-effective system. Approximately 1500 sugar beet DArT markers were developed in collaboration between NWISRL and DArT Company in Canberra, Australia. These DArT markers provide a ready to use platform available for scientists to genotype sugar beet and conduct in-depth molecular genetics research to identify genes of interest. Currently they are used by other groups to genotype sea beet.
Genetic linkage mapping
We identified DNA markers linked to beet curly top (BCT) resistance genes. A major single QTL was identified in chromosome 7 linked to BCT resistance. This is the first public genetic linkage map of sugar beet based on DArT and targeted beet curly top. The RILs of this population will be used for field screening, QTL analysis, and to establish the inheritance of BCT resistance.
Drought and Frost tolerance
In collaboration with scientists in this laboratory we established a field irrigation regimes to screen germplasm for drought stress, water use efficiency, and proline accumulation. This research was conducted in cooperation with the seed company KWS-SAAT AG, Germany.
Frost can be a significant limitation to emergence and cause total damage of seedlings. We are using a simplified approach to screen germplasm for tolerance to frost damage at the seedling stage.
Postharvest storage can be for an extended period of 90-120 days. Therefore, all breeding populations, selected germplasm are analyzed for postharvest qualities before and after storage. We use outdoor and indoor commercial facilities for experimentation in addition to a small better-controlled indoor storage at our location.
We used Ethylmethane Sulfonate (EMS) in our lab. and Gamma-rays at the facilities of the International Atomic Energy Agency (IAEA-Vienna, Austria) to generate mutants from the USDA-ARS Kimberly germplasm. More than 5000 mutants are under screening for economically important traits in an effort to broaden the genetic-base and prevent a genetic bottleneck in sugar beet.
We received grants for all research proposals submitted to the funding and stakeholders bodies interested in sugar beet research since 2008.
International collaboration and material transfer agreements