Kevin C. Falk

Characteristics of Starch from Eight Quinoa Lines

ABSTRACT Starches ranging in amylose content from 3 to 20% from eight quinoa (Chenopodium quinoa Willd.) lines were characterized with respect to thermal, retrogradation, and pasting properties; swelling and solubility behavior; freeze-thaw stability; water-binding capacity; shear stability; and granule size and morphology. The starches differed in gelatinization onset temperatures, peak temperatures, and retrogradation tendencies; these characteristics were positively correlated with amylose content. No variation in gelatinization enthalpy was observed. With the exception of pasting temperature, large variations in pasting characteristics were found among starches and were correlated with amylose content. Swelling, solubility, freeze-thaw stability, and water-binding capacity also differed among starches and were correlated with amylose content. Granule morphology and size were similar for all starches. The wide variation in amylose content and physicochemical characteristics of quinoa starches suggests ...

Genetics and breeding for clubroot resistance in Canadian spring canola (Brassica napus L.)

Abstract Clubroot disease caused by Plasmodiophora brassicae Woronin is a concern to the canola (Brassica napus L.) growers in Canada. A crop management strategy that includes deployment of genetic resistance and appropriate cultural practices is needed for long-term management of this disease. Resistance to the P. brassicae pathotypes present in Canada has been found in the primary and secondary gene pools of spring B. napus canola. Some of these sources, such as winter canola ‘Mendel’, rutabaga and Pak Choi (Brassica rapa L.) ‘Flower Nabana’, were used in genetic studies and breeding for the development of clubroot-resistant canola cultivars. A dominant gene in ‘Mendel’ and ‘Flower Nabana’ was found to confer resistance to P. brassicae pathotype 3, while a simple or a complex genetic control of resistance was found in rutabaga. The clubroot resistance (CR) gene in ‘Flower Nabana’ was mapped to chromosome A3, and molecular markers linked to the CR gene were identified for use in marker-assisted breeding (MAB). Using the CR genes from ‘Mendel’ and rutabaga, several clubroot-resistant spring canola lines were developed. Often the CR genes of ‘Mendel’ and rutabaga conferring resistance to pathotype 3 also conferred resistance to other pathotypes of P. brassicae found in Canada, including pathotypes 5, 6 and 8. The CR gene of ‘Flower Nabana’ was introgressed into B. napus and B. rapa canola through MAB. Since single-gene controlled resistance can be eroded, other strategies such as pyramiding different CR genes into B. napus canola should be considered for durable resistance.

Camelina seed quality in response to applied nitrogen, genotype and environment

Jiang, Y., Caldwell, C. D. and Falk, K. C. 2014. Camelina seed quality in response to applied nitrogen, genotype and environment. Can. J. Plant Sci. 94: 971-980. Camelina (Camelina sativa L.), Brassicaceae, has great potential for food and industrial use. This study analyzed the seed oil content, oil yield, protein content, protein yield, as well as fatty acid profile relative to varying nitrogen (N) rates and in different genotypes under several environmental conditions. Seed samples were obtained from a 2-yr field study with five environments (site-years), five genotypes, and six N rates. Applied N increased protein content, protein yield, oil yield, and polyunsaturated fatty acids (PUFA), but decreased oil content and monounsaturated fatty acids (MUFA). Saturated fatty acids did not respond consistently to applied N. Lower air temperatures during the reproductive stages increased the total seed oil content, but the fatty acid composition was not affected. The experimental line CDI007 had the highest oil content, oil yield, protein yield, and PUFA, but contained the lowest protein content and MUFA. CDI002 contained the highest protein content and PUFA. CDI005 had the highest amount of MUFA. CDI008 was not considered to be a promising genotype since it had the lowest oil content and highest amount of saturated fatty acids.

Water-stress and N-nutrition effects on photosynthesis and growth of Brassica carinata

Effects of water and nitrogen (N) supply on growth and photosynthetic response of B. carinata were examined in this study. Plant growth and related characteristics varied significantly in response to the availability of water and nitrogen. B. carinata maximized the utilization efficiency of the most limiting resources by developing physiological adaptations, such as changes in root and leaf development. The utilization of water and N was tightly linked with the availability of each resource. Instantaneous water-use efficiency (WUE) was always greater in plants with high-N nutrition [50, 100, and 150 kg(N) ha−1] than in the low-N-treated plants [0 kg(N) ha−1] in all watering treatments. Instantaneous N-use efficiency (PNUE) decreased significantly with increasing water stress in all N treatments. Seed yield is significantly related to PNUE (p>0.05) but not WUE (p<0.05). The positive relationship between leaf net photosynthetic rate (PN) and seed yield suggests that PN can be used as an important tool for selection of new strains with high seed yield.

Sources of resistance to Plasmodiophora brassicae (clubroot) pathotypes virulent on canola

Abstract A collection of 955 Brassica accessions including B. rapa (718), B. napus (94), B. juncea (93), B. oleracea (30), B. carinata (12) and B. nigra (8) was screened against Plasmodiophora brassicae pathotype 3 (1 × 106 resting spores cc−1 growth medium), the predominant strain of the pathogen on canola in western Canada. A total of 35 accessions (mostly B. rapa) showed at least 50% reduced clubroot severity relative to a susceptible control, with 15 showing complete resistance (clubroot-free). Ten resistant accessions representing Brassica A-, B- and C-genome species were tested further using a 10-fold higher pathogen inoculum dose (1 × 107 resting spores cc−1 growth medium) and by testing them against the five pathotypes (2, 3, 5, 6 and 8) of P. brassicae found in Canada. One B. nigra, two B. oleracea and four B. rapa (oriental vegetable) accessions maintained a high level of resistance under the higher pathogen inoculum pressure, while one B. nigra and two B. rapa (turnip) accessions showed moderate resistance. Most of the selected clubroot-resistant accessions showed consistent resistance to each of the five P. brassicae pathotypes found in Canada, except for one B. nigra and two turnip accessions, which varied slightly against different pathotypes. Several promising sources of clubroot resistance were identified in this study that can be used to develop new canola germplasm with a diverse clubroot resistance background for potentially more durable clubroot resistance.

Photosynthetic and growth responses of Camelina sativa (L.) Crantz to varying nitrogen and soil water status

Water and nitrogen (N) deficiency are two major constraints limiting the yield and quality of many oilseed crops worldwide. This study was designed to assess the response of Camelina sativa (L.) Crantz to the availability of N and water resources on photosynthesis and yield parameters. All the measured variables, which included plant height, root and shoot dry matter, root:shoot ratio, xylem pressure potential (XPP), yield components, photosynthetic parameters, and instantaneous water-use efficiency (WUE) were remarkably influenced by water and nitrogen supply. Net photosynthetic rate (PN) and yield components were significantly decreased more by water deficit than by N deficiency. XPP, stomatal conductance (gs), and intercellular CO2 concentration (Ci) decreased substantially as the water deficit increased irrespective of the level of N application. WUE at the high N supply [100 and 150 kg(N) ha−1] dropped in a large degree as the increased water deficit due to a larger decrease in PN than transpiration rate (E). The results of this study suggest that the regulative capacity of N supply on photosynthetic and plant growth response is significantly affected by soil water status and C. sativa is more sensitive to water deficit than N supply.

Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing.

Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar “Flower Nabana”. In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker-assisted introgression of Rcr1 into B. napus canola from B. rapa, with 100% accuracy in this study.

Genotyping-by-sequencing reveals three QTL for clubroot resistance to six pathotypes of Plasmodiophora brassicae in Brassica rapa

Clubroot, caused by Plasmodiophora brassicae, is an important disease of Brassica crops worldwide. F1 progeny from the Brassica rapa lines T19 (resistant) × ACDC (susceptible) were backcrossed with ACDC, then self-pollinated to produce BC1S1 lines, From genotyping-by-sequencing (GBS) of the parental lines and BC1 plants, about 1.32 M sequences from T19 were aligned into the reference genome of B. rapa with 0.4-fold coverage, and 1.77 M sequences with 0.5-fold coverage in ACDC. The number of aligned short reads per plant in the BC1 ranged from 0.07 to 1.41 M sequences with 0.1-fold coverage. A total of 1584 high quality SNP loci were obtained, distributed on 10 chromosomes. A single co-localized QTL, designated as Rcr4 on chromosome A03, conferred resistance to pathotypes 2, 3, 5, 6 and 8. The peak was at SNP locus A03_23710236, where LOD values were 30.3 to 38.8, with phenotypic variation explained (PVE) of 85–95%. Two QTLs for resistance to a novel P. brassicae pathotype 5x, designated Rcr8 on chromosome A02 and Rcr9 on A08, were detected with 15.0 LOD and 15.8 LOD, and PVE of 36% and 39%, respectively. Bulked segregant analysis was performed to examine TIR-NBS-LRR proteins in the regions harboring the QTL.

Differential metabolite profiles and salinity tolerance between two genetically related brown-seeded and yellow-seeded Brassica carinata lines

Brassica carinata (Ethiopian mustard) has previously been identified as a potential crop species suitable for marginal land in the North American prairies due to its relatively high salt tolerance. Two genetically related B. carinata lines with brown-seeded (BS) and yellow-seeded (YS) phenotypes were assessed for their tolerance to sodium sulfate. Specifically, each line was greenhouse-grown under 0, 50 and 100mM of salt, and analyzed after four weeks and eight weeks of treatment. Generally, the height of the BS line was greater than the YS line under both salt treatments, indicating enhanced salt tolerance of the BS line. NMR-based metabolite profiling and PCA analyses indicated a more pronounced shift in key stem metabolites after four weeks of treatment with the YS line compared to the BS line. For example, tryptophan and formate levels increased in the YS line after four weeks of 100mM salt treatment, while proline and threonine levels varied uniquely compared to other metabolites of the lines. Together, the data indicate that the brown-seeded line has greater sodium tolerance than the yellow-seed line, provide clues to the biochemical underpinnings for the phenotypic variation, and highlight the utility of B. carinata as a biorefinery crop for saline land.

Fine Mapping of a Clubroot Resistance Gene in Chinese Cabbage Using SNP Markers Identified from Bulked Segregant RNA Sequencing

Clubroot, caused by Plasmodiophora brassicae, is an important disease of canola (Brassica napus) in western Canada and worldwide. In this study, a clubroot resistance gene (Rcr2) was identified and fine mapped in Chinese cabbage cv. “Jazz” using single-nucleotide polymorphisms (SNP) markers identified from bulked segregant RNA sequencing (BSR-Seq) and molecular markers were developed for use in marker assisted selection. In total, 203.9 million raw reads were generated from one pooled resistant (R) and one pooled susceptible (S) sample, and >173,000 polymorphic SNP sites were identified between the R and S samples. One significant peak was observed between 22 and 26 Mb of chromosome A03, which had been predicted by BSR-Seq to contain the causal gene Rcr2. There were 490 polymorphic SNP sites identified in the region. A segregating population consisting of 675 plants was analyzed with 15 SNP sites in the region using the Kompetitive Allele Specific PCR method, and Rcr2 was fine mapped between two SNP markers, SNP_A03_32 and SNP_A03_67 with 0.1 and 0.3 cM from Rcr2, respectively. Five SNP markers co-segregated with Rcr2 in this region. Variants were identified in 14 of 36 genes annotated in the Rcr2 target region. The numbers of poly variants differed among the genes. Four genes encode TIR-NBS-LRR proteins and two of them Bra019410 and Bra019413, had high numbers of polymorphic variants and so are the most likely candidates of Rcr2.