September 29, 2020

Quarterly Report – September 2012

Two-page executive summary

Genotyping: SNP Genotyping: The barley iSelect 9,000 SNP barley chip was cross-referenced with previous chips, automatic SNP calling procedures were implemented and the SNP metadata were expanded. The TCAP wheat group mapped 7,517 SNPs from the previous 9,000 SNP wheat chip and played a key role in the development of a new 90,000 SNP wheat chip. Genotyping of the barley and wheat association mapping panels, elite breeding germplasm, and genomic selection populations is on target.

New genotyping technologies: The Nimblegen whole exome capture assays targeting 110 Mb of sequence in the wheat genome and 90 Mb of sequence in the barley genome have been designed and tested with promising results (77% of sequence reads mapped to the references and more than 90% of targeted exonic regions were represented). The previous results were used to design new rebalanced beta versions that are now being tested. Genotyping by sequencing (GBS) was expanded into new mapping populations generating thousands of polymorphic GBS tags and high-density maps.

The Triticeae toolbox database (T3): New phenotypic and genotypic datasets were incorporated into T3. The user interface was improved to enable more intuitive data searches and the integration of multiple datasets. Three online tutorials explaining data submission to T3 have been developed. Hyperlinks to other databases were created to facilitate users tracking down information about lines or markers. T3 now uses two-dimensional “materialized view” tables to access genotype data. This approach provides quicker access to large blocks of data as well as more compact storage.

Phenotyping: During this period we made significant improvements in the canopy spectral reflectance protocols: improved equipment configurations, developed a more precise measurement protocol and implemented scripts to facilitate the management and analysis of data. This technology was used to evaluate the National Small Grain Collection (NSGC) core collections of barley (500 six-row spring accessions) and wheat (540 spring wheat accessions). The best drought resistant lines from the NSGC screen from 2011 have been incorporated into the wheat breeding programs.

Water use efficiency (WUE): In barley, four association mapping populations were evaluated for WUE at six locations and one was planted for seed increase. In wheat, two association mapping panels were evaluated in five (spring) and three (winter) locations for agronomic and physiological traits, including canopy spectral reflectance data. Eight additional specialized wheat mapping populations were phenotyped for root characteristics, physiological traits associated with WUE, heat stress, and agronomic performance. The chromosome region defining drought tolerance in the rye 1RS translocation was identified and the beneficial effect of photoperiod sensitivity in early planting rain-fed northern latitudes was validated.

Nitrogen use efficiency (NUE): In barley, NUE was evaluated using the spring six-row (SP6), spring two-row (SP2), and winter six-row (WN6) association mapping panels in low (70%) nitrogen and normal (100%) nitrogen in three environments. Results are being analyzed and incorporated into T3. In wheat, both the hard and soft winter wheat panels were evaluated for NUE at two locations (at different N levels) and in four additional locations for yield. The genotyping of all these lines with the iSelect 90,000 SNP wheat chip is on track to be completed before the end of 2012.

Disease resistance: In barley, the NSGC was evaluated for resistance to spot blotch, spot form net blotch and stripe rust. Seventeen accessions resistant to the highly virulent isolate ND4008 of the spot blotch pathogen (Cochliobolus sativus) were identified. Nine lines were identified that are highly resistant to current virulent isolates of spot form net blotch from North Dakota, Australia, New Zealand, and Denmark. In wheat, the analyses of the 2011 and 2012 data for leaf, stem, and stripe rust (1000 spring lines) resulted in the identification of multiple resistance loci for the three diseases, which are being validated by backcrossing into a common susceptible line. Seedling screening of the complete core collection for the three rusts will be completed before the end of 2012.

Population development: The spring wheat Nested Association Mapping (NAM) population was completed and the barley and winter wheat NAM populations were advanced as planned. The development of the wild barley introgression population was completed and genotyped with a custom 384 SNP assay.

Education: A total of 69 graduate students (Appendix H3) have participated in the plant breeding training network. Sixty-two are directly mentored by a TCAP PI, with 38 students being funded by TCAP. Fifty-five undergraduates (Appendix H4) have participated in the TCAP with 37 being mentored by TCAP faculty and graduate students. Additionally, 17 students from Minority Serving Institutions (MSI) are being mentored MSI faculty.

Plant Breeding Training Network (PBTN): The online environment was used to deliver and archive three courses, including Plant Breeding Strategies, Entering Mentoring, and Quantitative Genetics. To insure sustainability of course offerings, the development of an online Plant Breeding Program through Ag*Idea was initiated. Undergraduate students have been supported in their development through three online meetings with industry representatives and TCAP PIs. The development of three undergraduate educational tools has continued and one tool was submitted to an education journal. The PBTN also has been used as a communication tool for project management both for the TCAP, Ag*Idea Executive Committee, and the National Association of Plant Breeders graduate student committee.

Newsletters, films and other communication resources: Information about research and education was shared both internally and externally through six meetings of the TCAP seminar series. Other communication tools include the quarterly newsletters and the face to face meetings at PAG. The TCAP produced film “Holding the future in the palm of your hand” was shown during three recruiting trips to about 200 students. Two of these students applied to TCAP graduate schools. Minority students have been attracted to several internships. The first year evaluation report was received and used to guide second year planning. Evaluation tools were also refined.

Publications and germplasm releases: TCAP participants generated 35 peer reviewed publications during the first 8 months of 2012, which exceeds the total number of publications for the complete first year, which shows accelerated progress. In addition, ten new wheat varieties and two wheat germplasm were released (initiated in previous BarleyCAP and WheatCAP and completed in TCAP).