Plant Sciences

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    Dry Edible Bean White Mold MAGIC Population
    (2021) Escobar, Edgar; Oladzad, Atena; Simons, Kristin J.; Lee, Rian; Schroder, Stephan; McClean, Phillip E.; Osorno, Juan M.
    A dry edible bean MAGIC population was generated to map genes for resistance to white mold and to produce inbred lines with improved white mold (WM) resistance combined with good agronomic performance for primarily the pinto bean market class. Eight founding parents were crossed to develop a modified MAGIC population. PT7-2 was intermated with Powderhorn (cross A). ID14-4 was intermated with CO16079 (cross B). La Paz was intermated with Lariat (cross C). USPT-WM_12 was intermated with El Dorado (cross D). Subsequently, F1 plants of each initial cross were intermated using a one-way funnel, F1 from cross A was mated with F1 from cross B and F1 from cross C was mated with F1 from cross D meaning that not every possible cross combination was conducted. The next cycle consisted of intermating F1 from the AxB cross with F1 from the CxD cross. For each cycle reciprocal crosses were conducted to offset potential maternal effects and maternal inheritance. After the final crosses, the F1 were planted to produce the F2 generation which then went through three rounds of single seed descent from F2 to F5. A total of 1,050 F2-derived F5 inbred lines were developed for this WM-MAGIC population. A total of 428 lines representing each of the crosses were assigned to the training population. The remaining lines were assigned to the validation population. The training population has been genotyped. Briefly, the DNA was isolated from each line and sequenced using a single-end Illumina platform. Sequences were quality trimmed using SICKLE and then aligned to the Phaseolus vulgaris v2.1 reference sequence (DOE-JGI and USDA-NIFA, http://phytozome.jgi.doe.gov) or the UI111 v1.0 reference sequence, indexed and sorted using BWA-MEMB and SAMtools. Read groups including library ID, platform and platform unit were added to each alignment within the BAM files using Picard. Unifiedgenotyper from GATK3.6 (DePristo et al. 2011) was used to call variants with quality scores above 10. Quality scores between 10 and 30 were marked as low quality. Variants with a read depth of less than two were filtered using GATK3.6 variantfiltration and subsequently replaced as missing data. Low quality variants were removed via hard filtering when variants contained more than 25% missing data, more than one nucleotide, or the minor allele was less than 1%. Genotypes with more than 90% missing data were removed. SNPs with missing data were imputed using fastPHASE. The output file was converted to a hmp file for distribution. Lines were phenotyped using the seedling straw test method proposed by Arkwazee and Myers (2017). The plants were scored four days after inoculation using the disease severity scale described in the protocol. Lines were considered resistant with values from 1 to 3, intermediate with a value of 4, and susceptible with values from 5 to 9. Adjusted means (least square means) were calculated using a linear mixed model in which genotypes were considered fixed effects and reps, blocks, and samples were considered random effects.
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    Malting Barley: Contribution of Minnesota and North Dakota to the Soul of Beer with Dr. Paul Schwarz, September 10, 2020
    (North Dakota State University. Libraries, 9/10/2020) Schwarz, Paul B.; North Dakota State University. Libraries
    This event was hosted by NDSU Libraries. The presentation was pre-recorded and then shared on NDSU Libraries’ Facebook page.
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    MulchH2O Project Data
    (2023) Gramig, Greta G.
    Polyethylene plastic mulch is widely used in organic horticultural systems to suppress weeds and promote crop performance through optimization of soil temperature and moisture. Unfortunately, disposal of this non-biodegradable material is associated with negative environmental impacts that are misaligned with goals of organic agriculture. We propose to develop biodegradable alternative mulches that effectively suppress weeds, but also enhance or maintain soil health while mitigating plastic pollution.
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    Using Breeding Populations With a Dual Purpose: Cultivar Development and Gene Mapping—A Case Study Using Resistance to Common Bacterial Blight in Dry Bean (Phaseolus vulgaris L.)
    (2021) Simons, Kristin J.; Oladzad, Atena; Lamppa, Robin; Maniruzzaman; McClean, Phillip E.; Osorno, Juan M.; Pasche, Julie S.
    Dry bean (Phaseolus vulgaris L.) is an important worldwide legume crop with low to moderate levels of resistance to common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli. A total of 852 genotypes (cultivars, preliminary and advanced breeding lines) from the North Dakota State University dry bean breeding program were tested for their effectiveness as populations for genome-wide association studies (GWAS) to identify genomic regions associated with resistance to CBB, to exploit the associated markers for marker-assisted breeding (MAB), and to identify candidate genes. The genotypes were evaluated in a growth chamber for disease resistance at both the unifoliate and trifoliate stages. At the unifoliate stage, 35% of genotypes were resistant, while 25% of genotypes were resistant at the trifoliate stage. Libraries generated from each genotype were sequenced using the Illumina platform. After filtering for sequence quality, read depth, and minor allele frequency, 41,998 single-nucleotide polymorphisms (SNPs) and 30,285 SNPs were used in GWAS for the Middle American and Andean gene pools, respectively. One region near the distal end of Pv10 near the SAP6 molecular marker from the Andean gene pool explained 26.7–36.4% of the resistance variation. Three to seven regions from the Middle American gene pool contributed to 25.8–27.7% of the resistance, with the most significant peak also near the SAP6 marker. Six of the eight total regions associated with CBB resistance are likely the physical locations of quantitative trait loci identified from previous genetic studies. The two new locations associated with CBB resistance are located at Pv10:22.91–23.36 and Pv11:52.4. A lipoxgenase-1 ortholog on Pv10 emerged as a candidate gene for CBB resistance. The state of one SNP on Pv07 was associated with susceptibility. Its subsequent use in MAB would reduce the current number of lines in preliminary and advanced field yield trial by up to 14% and eliminate only susceptible genotypes. These results provide a foundational SNP data set, improve our understanding of CBB resistance in dry bean, and impact resource allocation within breeding programs as breeding populations may be used for dual purposes: cultivar development as well as genetic studies.