Alireza Navabi

Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations

BackgroundCommon bacterial blight (CBB), incited by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Host resistance is practically the most effective and environmentally-sound approach to control CBB. Unlike conventional QTL discovery strategies, in which bi-parental populations (F2, RIL, or DH) need to be developed, association mapping-based strategies can use plant breeding populations to synchronize QTL discovery and cultivar development.ResultsA population of 469 dry bean lines of different market classes representing plant materials routinely developed in a bean breeding program were used. Of them, 395 lines were evaluated for CBB resistance at 14 and 21 DAI (Days After Inoculation) in the summer of 2009 in an artificially inoculated CBB nursery in south-western Ontario. All lines were genotyped using 132 SNPs (Single Nucleotide Polymorphisms) evenly distributed across the genome. Of the 132 SNPs, 26 SNPs had more than 20% missing data, 12 SNPs were monomorphic, and 17 SNPs had a MAF (Minor Allelic Frequency) of less than 0.20, therefore only 75 SNPs were used for association study, based on one SNP per locus. The best possible population structure was to assign 36% and 64% of the lines into Andean and Mesoamerican subgroups, respectively. Kinship analysis also revealed complex familial relationships among all lines, which corresponds with the known pedigree history. MLM (Mixed Linear Model) analysis, including population structure and kinship, was used to discover marker-trait associations. Eighteen and 22 markers were significantly associated with CBB rating at 14 and 21 DAI, respectively. Fourteen markers were significant for both dates and the markers UBC420, SU91, g321, g471, and g796 were highly significant (p ≤ 0.001). Furthermore, 12 significant SNP markers were co-localized with or close to the CBB-QTLs identified previously in bi-parental QTL mapping studies.ConclusionsThis study demonstrated that association mapping using a reasonable number of markers, distributed across the genome and with application of plant materials that are routinely developed in a plant breeding program can detect significant QTLs for traits of interest.

Organic and conventional management of mixtures of wheat and spring cereals

Cereal mixtures may provide both organic and conventional producers with a more sustainable approach in reducing weed pressure, crop rotation flexibility, improved yield stability, buffering against pests and diseases, minimizing soil variability and increasing animal feed value. We examined the response of small grain mixtures containing wheat, oats, barley and triticale to varying degrees of natural competition and environmental stress at three locations in central Alberta, Canada. One modern and one heritage hard-red spring wheat cultivar, along with one cultivar each of oats, barley and triticale and eighteen two-way mixtures, were planted on organic and conventional land at seven location-years between 2003 and 2005. Average yields were 30% to 70% lower on organically managed sites. Monocrop barley yielded 43% and 16% higher than the site average at two organic locations. Our results suggest two main conclusions: (1) on conventionally managed land, wheat-barley mixtures exhibited potential for yield maintenance and weed suppression, and; (2) on organically managed land, competition with weeds had a large negative effect on yield (>30%). The 25:75 mixtures of wheat and oats, and all mixtures of Park (a heritage) wheat and Manny barley exhibited yield potential similar to or (up to 1.0 t ha−1) greater than monocrop yield. Manny barley mixtures exhibited weed suppressive capabilities.

Performance and stability of performance of spring wheat variety mixtures in organic and conventional management systems in western Canada

Wheat ( Triticum aestivum L.) variety mixtures represent a relatively unexplored avenue for maintaining and stabilizing yield for both organic and conventional producers. The present study examined the responses of three Canadian western red spring wheat varieties in sole crop and in variety mixtures to varying levels of simulated and natural competition, as well as environmental stress at one conventionally and two organically managed locations in central Alberta, Canada, between 2003 and 2005. Three modern hard red spring wheat varieties (Superb, semi-dwarf; AC Intrepid, early maturing and 5600HR, tall), along with 13 two- and three-way variety mixtures, were planted under two levels of simulated weed ( Brassica juncea L.) competition at each of the eight location-years. The B. juncea weed competition treatment decreased yields at all locations. Overall yield was lowest at the certified organic farm and highest under conventional management. Sole-crop semi-dwarf Superb and all three Superb–Intrepid mixture entries consistently yielded among the highest, regardless of management system, testing location or competition treatment. The 1:1 and 1:2 Superb–Intrepid mixture entries were the most stable of all entries tested. Early season vigour was strongly associated with yield, with the strongest correlation occurring under low-moisture, low-nutrient, high-competition conditions at the certified organic farm. Spring wheat variety mixtures may provide greater stability with little or no reduction in yield, while providing greater competitive ability.

Application of Image Analysis in Studies of Quantitative Disease Resistance, Exemplified Using Common Bacterial Blight–Common Bean Pathosystem

The effectiveness of image analysis (IA) compared with an ordinal visual scale, for quantitative measurement of disease severity, its application in quantitative genetic studies, and its effect on the estimates of genetic parameters were investigated. Studies were performed using eight backcross-derived families of common bean (Phaseolus vulgaris) (n = 172) segregating for the molecular marker SU91, known to be associated with a quantitative trait locus (QTL) for resistance to common bacterial blight (CBB), caused by Xanthomonas campestris pv. phaseoli and X. fuscans subsp. fuscans. Even though both IA and visual assessments were highly repeatable, IA was more sensitive in detecting quantitative differences between bean genotypes. The CBB phenotypic difference between the two SU91 genotypic groups was consistently more than fivefold for IA assessments but generally only two- to threefold for visual assessments. Results suggest that the visual assessment results in overestimation of the effect of QTL in genetic studies. This may have been caused by lack of additivity and uneven intervals of the visual scale. Although visual assessment of disease severity is a useful tool for general selection in breeding programs, assessments using IA may be more suitable for phenotypic evaluations in quantitative genetic studies involving CBB resistance as well as other foliar diseases.

Identification of candidate genes associated with CBB resistance in common bean HR45 (Phaseolus vulgaris L.) using cDNA-AFLP

Common bacterial blight (CBB), incited by Xanthomonas axonopodis pv. phaseoli (Xap), is a serious seed-borne disease of common bean (Phaseolus vulgaris L.) in both temperate and tropical production zones. The line HR45 is highly resistant to Xap infection on leaves and pods in both field and greenhouse. To understand the molecular mechanisms underlying CBB resistance in HR45, cDNA-amplified fragment length polymorphism (AFLP) technique was used to identify the genes that are differentially expressed in the leaves of HR45 at different time-periods after inoculation. Selective amplifications with 34 primer combinations allowed the visualization of 2,448 transcript-derived fragments (TDFs) in infected leaves, and 259 (10.6%) of them were differentially expressed TDFs (DE-TDFs). Seventy-seven of the DE-TDFs were cloned and sequenced. Thirty-nine of the 77 (50.6%) DE-TDFs representing bean transcripts were not previously reported in any EST database. The expression patterns of 10 representative DE-TDFs were further confirmed by real-time RT-PCR. BLAST analysis suggested that 40% (31 of 77) of the DE-TDFs were homologous to the genes related to metabolism, photosynthesis, and cellular transport, whereas 28% (22 of 77) of the DE-TDFs showed homology to the genes involved in defence response, response to stimulus, enzyme regulation, and transcription regulation. Thus, the 22 pathogenesis-related DE-TDFs were selected as potential functional candidate genes (FCGs) in association with CBB resistance. Meanwhile, six of the DE-TDFs (1FCG and five other DE-TDFs) were in silico mapped to the distal region of the bean linkage group B6 (the genomic location containing the major CBB resistance QTL in HR45) and, therefore, were considered as positional candidate genes (PCGs). This study represents a first step towards the discovery of bean genes expressed upon Xap infection. This information will be useful for elucidating the molecular basis of the resistance response process and identifying the genes that underlie the CBB-resistance.

The relationship between lodging and plant height in a diverse wheat population

We examined the genetic variation for lodging tolerance in different plant height groups, within a diverse population of wheat (Triticum aestivum L.) genotypes (n = 14 0). Lodging was artificially induced by dragging a weighted apparatus across plots twice during the season at early and late milk stages. Grain yield was negatively correlated with lodging, while lodging scores were positively correlated with plant height. Although plant height appeared to be the major contributor to lodging tolerance, some variation was also observed in taller plants. This suggests that genetic gain in lodging tolerance can be obtained, to some extent, independent of plant height. Key words: Plant height, lodging tolerance, Triticum aestivum L., CIMMYT, Canada

A genetic examination of early flowering and maturity in Canadian spring wheat

Under short-season western Canadian growing conditions, vernalization non-responsiveness is generally considered a preferable spring wheat (Triticum aestivum L.) phenotype, to avoid inconsistent maturity and yield patterns. The objectives of this study were to investigate the genetic factors affecting early flowering and maturity, and related agronomic traits, in a set of five Canadian spring wheat cultivars. The cultivars were first studied under 10- and 16-h photoperiods and 0- and 42-d vernalization treatments. Thereafter, the parents and F1 hybrids from a one-way diallel mating design were grown with and without a 42-d vernalization treatment. Shorter photoperiod delayed flowering time in all cultivars, and increased final leaf number in AC Barrie. Vernalization hastened flowering and decreased final leaf number in AC Foremost and AC Taber. AC Foremost and AC Taber carry at least one different allele, from the rest of the cultivars studied, at the major loci governing vernalization response. Leaf and ...

QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers

We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars ‘Cutler’ and ‘AC Barrie’ using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using microsatellite and DArT markers. Results from this study provide additional information to wheat researchers developing early maturing and short stature spring wheat cultivars.

A genetic analysis of weed competitive ability in spring wheat.

Competition with weeds decreases crop yields globally. Breeding for competitive ability against elevated weed pressure can be difficult because the selection for specific traits which contribute to competitive ability may result in yield losses. The widely studied International Triticeae Mapping Initiative (ITMI) population was used to study the genetics of traits associated with competitive ability in a high latitude (52-53oN) wheat-growing environment in central Alberta, Canada. Grain yield without weed competition and under experimentally sown cultivated oat competition exhibited similar heritability. Grain yield was positively correlated with early season vigour, and negatively correlated with days to maturity in the competitive treatment only. In this study, similar heritability estimates between competition treatments suggest that selection in a weed free environment can lead to improvements in a weedy environment, but some high-yielding lines under competition would be eliminated during selection.K...

N2 fixation ability of different dry bean genotypes

Farid, M. and Navabi, A. 2015. N2 fixation ability of different dry bean genotypes. Can. J. Plant Sci. 95: 1243-1257. Common bean (Phaseolous vulgaris L.) is generally known as a weak N2 fixer compared with other legumes. The availability of genetic variation for N2 fixation potential of common bean supports the idea that symbiotic nitrogen fixation (SNF) in common bean can be improved through breeding. To assess the potential N2 fixation of selected common bean genotypes, 12 bean varieties including three Andean and nine Middle American were screened for SNF ability and related traits in controlled environments and field trials in Ontario, Canada. A non-nodulating mutant, R99, was used as the reference plant to estimate nitrogen derived from the atmosphere (Ndfa) through the natural 15N abundance method. Significant variation was found among the bean genotypes for Ndfa and its related traits. Environmental and genotype by environmental effects significantly influenced Ndfa and its related traits. The three Andean bean genotypes were superior to Middle American genotypes for nodulation ability, while the Middle American genotypes were generally stronger nitrogen fixers in optimum soil moisture conditions. In general, nitrogen fixation was found to be significantly associated with seed yield and carbon isotope discrimination, an indicator of water use efficiency.