Thermal processing methods differentially affect the protein quality of Chickpea (Cicer arietinum)

Chickpea is a widely produced pulse crop, but requires processing prior to human consumption. Protein bioavailability and amino acid quantity of chickpea flour can be altered by multiple factors including processing method. For this reason, the protein quality of processed chickpea flour was determined using in vivo and in vitro analyses for processed chickpeas. Processing differentially affected the protein digestibility-corrected amino acid score (PDCAAS) of chickpeas with extruded chickpea (83.8) having a higher PDCAAS score than both cooked (75.2) and baked (80.03). Interestingly, the digestible indispensable amino acid score (DIAAS) value of baked chickpea (0.84) was higher compared to both extruded (0.82) and cooked (0.78). The protein efficiency ratio, another measure of protein quality, was significantly higher for extruded chickpea than baked chickpea (p < .01). In vivo and in vitro analysis of protein quality were well correlated (R 2 = .9339). These results demonstrated that under certain circumstances in vitro methods could replace the use of animals to determine protein quality.

Integrating genomics for chickpea improvement: achievements and opportunities

Integration of genomic technologies with breeding efforts have been used in recent years for chickpea improvement. Modern breeding along with low cost genotyping platforms have potential to further accelerate chickpea improvement efforts. The implementation of novel breeding technologies is expected to contribute substantial improvements in crop productivity. While conventional breeding methods have led to development of more than 200 improved chickpea varieties in the past, still there is ample scope to increase productivity. It is predicted that integration of modern genomic resources with conventional breeding efforts will help in the delivery of climate-resilient chickpea varieties in comparatively less time. Recent advances in genomics tools and technologies have facilitated the generation of large-scale sequencing and genotyping data sets in chickpea. Combined analysis of high-resolution phenotypic and genetic data is paving the way for identifying genes and biological pathways associated with breeding-related traits. Genomics technologies have been used to develop diagnostic markers for use in marker-assisted backcrossing programmes, which have yielded several molecular breeding products in chickpea. We anticipate that a sequence-based holistic breeding approach, including the integration of functional omics, parental selection, forward breeding and genome-wide selection, will bring a paradigm shift in development of superior chickpea varieties. There is a need to integrate the knowledge generated by modern genomics technologies with molecular breeding efforts to bridge the genome-to-phenome gap. Here, we review recent advances that have led to new possibilities for developing and screening breeding populations, and provide strategies for enhancing the selection efficiency and accelerating the rate of genetic gain in chickpea.

Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.)

Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD_1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.

A reference genome for pea provides insight into legume genome evolution

We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

Correction to: Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.)

Unfortunately there was an error in the name of the gene "Ca-AKL18" in the discussion section.

Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.)

A high-density linkage map of chickpea using 3430 SNPs was constructed and used to identify QTLs and candidate genes for ascochyta blight resistance in chickpea. Chickpea cultivation in temperate conditions is highly vulnerable to ascochyta blight infection. Cultivation of resistant cultivars in combination with fungicide application within an informed disease management package is the most effective method to control ascochyta blight in chickpeas. Identifying new sources of resistance is critical for continued improvement in ascochyta blight resistance in chickpea. The objective of this study was to identify genetic loci and candidate genes controlling the resistance to ascochyta blight in recombinant inbred lines derived from crossing cultivars Amit and ICCV 96029. The RILs were genotyped using the genotyping-by-sequencing procedure and Illumina^® GoldenGate array. The RILs were evaluated in the field over three site-years and in three independent greenhouse experiments. A genetic map with eight linkage groups was constructed using 3430 SNPs. Eight QTLs for resistance were identified on chromosomes 2, 3, 4, 5 and 6. The QTLs individually explained 7-40% of the phenotypic variations. The QTLs on chromosomes 2 and 6 were associated with the resistance at vegetative stage only. The QTLs on chromosomes 2 and 4 that were previously reported to be conserved across diverse genetic backgrounds and against different isolates of Ascochyta rabiei were confirmed in this study. Candidate genes were identified within the QTL regions. Their co-localization with the underlying QTLs was confirmed by genetic mapping. The candidate gene-based SNP markers would lead to more efficient marker-assisted selection for ascochyta blight resistance and would provide a framework for fine mapping and subsequent cloning of the genes associated with the resistance.

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

Whole-genome sequencing-based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the application of next-generation sequencing (NGS)-based BSA approach for mapping QTLs for ascochyta blight resistance in chickpea using two recombinant inbred line populations CPR-01 and CPR-02. Eleven QTLs in CPR-01 and six QTLs in CPR-02 populations were mapped on chromosomes Ca1, Ca2, Ca4, Ca6 and Ca7. The QTLs identified in CPR-01 using conventional biparental mapping approach were used to compare the efficiency of NGS-based BSA in detecting QTLs for ascochyta blight resistance. The QTLs on chromosomes Ca1, Ca4, Ca6 and Ca7 overlapped with the QTLs previously detected in CPR-01 using conventional QTL mapping method. The QTLs on chromosome Ca4 were detected in both populations and overlapped with the previously reported QTLs indicating conserved region for ascochyta blight resistance across different chickpea genotypes. Six candidate genes in the QTL regions identified using NGS-based BSA on chromosomes Ca2 and Ca4 were validated for their association with ascochyta blight resistance in the CPR-02 population. This study demonstrated the efficiency of NGS-based BSA as a rapid and cost-effective method to identify QTLs associated with ascochyta blight in chickpea.

Determine effect of pressure heating on carbohydrate related molecular structures in association with carbohydrate metabolic profiles of cool-climate chickpeas using Globar spectroscopy

Grain has been heat-processed to alter rumen degradation characteristics and improve nutrient availabilities for ruminants. However, limited study was found on internal structure changes induced by processing on a molecular basis. The objectives of this study were to use advanced vibrational molecular spectroscopy to: (1) determine the processing induced carbohydrate (CHO) structure changes on a molecular basis, (2) investigate the effect of pressure heating on changes of CHO chemical profiles, CHO subfractions in cool-climate CDC Chickpea varieties, and (3) to reveal the association between carbohydrates related molecular spectra with carbohydrate metabolic profiles. The cool-climate CDC chickpea varieties with multisource were pressure heated in an autoclave at 120 °C for 60 min; and FTIR vibrational spectroscopy was used to detect the molecular spectra. Molecular spectroscopic results showed that compared to raw chickpea varieties, autoclave heating induced changes in both total CHO (region and baseline ca. 1186-946 cm^-1) and structural CHO (STCHO, region and baseline ca. 1482-1186 cm^-1), except for cellulosic compounds (CELC, region and baseline ca. 1374-1212 cm^-1). The CHO chemical profile and rumen degradation results showed that autoclave heating decreased rumen degradable, undegradable and intestinal digestible sugar (CA4) content, but increased available fiber (CB3) content, without affecting available energy of chickpeas. The changes of CHO molecular spectra in chickpea varieties were strongly correlated with CHO chemical profiles, CHO subfractions, and CHO rumen degradation characteristics. Moreover, the regression analysis showed that STCHO peak 1 height could be used to predict sugar content, its rumen degradability and digestibility of chickpeas. Our results suggest that autoclave heating markedly changes sugar and fiber degradation characteristics. The carbohydrate molecular spectral profiles are associated with carbohydrate metabolic profiles in raw and pressure heated cool-climate chickpeas.

Sensory Acceptability of Iron-Fortified Red Lentil (Lens culinaris Medik.) Dal

Panelists in Saskatoon, Canada (n = 45) and Dhaka, Bangladesh (n = 98) participated in sensory evaluations of the sensory properties of both cooked and uncooked dehulled red lentil dal fortified with FeSO₄ ·7H₂ O, NaFeEDTA or FeSO₄ ·H₂ O at fortificant Fe concentrations of 800, 1,600 (both cooked and uncooked), or 2,800 ppm. Appearance, odor, and overall acceptability of cooked and uncooked samples were rated using a 9-point hedonic scale (1 = dislike extremely to 9 = like extremely). Taste and texture were rated for the cooked samples prepared as typical south Asian lentil meals. Significant differences in sensory quality were observed among all uncooked and cooked samples at both locations. Overall, scores for all sensory attributes and acceptability of uncooked lentil decreased with increasing concentration of Fe in the fortificant; however, Fe fortification (particularly with NaFeEDTA) had small effects on acceptability. Panelists from Saskatoon provided a wider range of scores than those from Bangladesh for all attributes of cooked lentil. Overall, sensory evaluation of Fe fortification using NaFeEDTA minimally affected consumer perception of color, taste, texture, odor, and overall acceptability of cooked lentil. Reliability estimates (Cronbach's alpha [CA]) indicated that consumer scores were generally consistent for all attributes of all lentil samples (mean CA > 0.80). NaFeEDTA was found to be the most suitable Fe fortificant for lentil based on consumer acceptability. Consumption of 45 to 50 g of NaFeEDTA-fortified lentil (fortificant Fe concentration of 1,600 ppm) per day meets the estimated average requirements (EARs) of Fe for humans (10.8 to 29.4 mg).

PRACTICAL APPLICATION

Iron fortification of dehulled lentil dal may change organoleptic attributes that can influence consumer acceptability. Sensory evaluation by consumers helps to determine the effect on appearance, odor, taste, texture, and overall acceptability of fortified lentils. In this study, consumer acceptability was evaluated with panelists who consume lentil regularly. Panelists provided significantly different scores for 5 sensory attributes for 10 uncooked and 3 cooked lentil samples. Panelists reliably preferred NaFeEDTA as the most suitable Fe fortificant for dehulled lentils for 5 attributes. Overall, lentil dal fortified with NaFeEDTA can offer a simple and low-cost solution to human health problems associated with iron-related malnutrition.

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.

Genotypic variation in the response of chickpea to arbuscular mycorrhizal fungi and non-mycorrhizal fungal endophytes

Plant roots host symbiotic arbuscular mycorrhizal (AM) fungi and other fungal endophytes that can impact plant growth and health. The impact of microbial interactions in roots may depend on the genetic properties of the host plant and its interactions with root-associated fungi. We conducted a controlled condition experiment to investigate the effect of several chickpea (Cicer arietinum L.) genotypes on the efficiency of the symbiosis with AM fungi and non-AM fungal endophytes. Whereas the AM symbiosis increased the biomass of most of the chickpea cultivars, inoculation with non-AM fungal endophytes had a neutral effect. The chickpea cultivars responded differently to co-inoculation with AM fungi and non-AM fungal endophytes. Co-inoculation had additive effects on the biomass of some cultivars (CDC Corrine, CDC Anna, and CDC Cory), but non-AM fungal endophytes reduced the positive effect of AM fungi on Amit and CDC Vanguard. This study demonstrated that the response of plant genotypes to an AM symbiosis can be modified by the simultaneous colonization of the roots by non-AM fungal endophytes. Intraspecific variations in the response of chickpea to AM fungi and non-AM fungal endophytes indicate that the selection of suitable genotypes may improve the ability of crop plants to take advantage of soil ecosystem services.

The Chickpea Early Flowering 1 (Efl1) Locus Is an Ortholog of Arabidopsis ELF3

In climates that experience short growing seasons due to drought, heat, or end-of-season frost, early flowering is a highly desirable trait for chickpea (Cicer arietinum). In this study, we mapped, sequenced, and characterized Early flowering3 (Efl3), an ortholog of Arabidopsis (Arabidopsis thaliana) EARLY FLOWERING3 (ELF3) that confers early flowering in chickpea. In a recombinant inbred line population derived from a cross between CDC Frontier and ICCV 96029, this gene was mapped to the site of a quantitative trait locus on Ca5 that explained 59% of flowering time variation under short days. Sequencing of ELF3 in ICCV 96029 revealed an 11-bp deletion in the first exon that was predicted to result in a premature stop codon. The effect of this mutation was tested by transgenic complementation in the Arabidopsis elf3-1 mutant, with the CDC Frontier form of CaELF3a partially complementing elf3-1 while the ICCV 96029 form had no effect on flowering time. While induction of FLOWERING LOCUS T homologs was very early in ICCV 96029, an analysis of circadian clock function failed to show any clear loss of rhythm in the expression of clock genes in ICCV 96029 grown under continuous light, suggesting redundancy with other ELF3 homologs or possibly an alternative mode of action for this gene in chickpea. The 11-bp deletion was associated with early flowering in global chickpea germplasm but was not widely distributed, indicating that this mutation arose relatively recently.

Iron Fortification of Lentil (Lens culinaris Medik.) to Address Iron Deficiency

Iron (Fe) deficiency is a major human health concern in areas of the world in which diets are often Fe deficient. In the current study, we aimed to identify appropriate methods and optimal dosage for Fe fortification of lentil (Lens culinaris Medik.) dal with FeSO₄·7H₂O (ferrous sulphate hepta-hydrate), NaFeEDTA (ethylenediaminetetraacetic acid iron (III) sodium salt) and FeSO₄·H₂O (ferrous sulphate mono-hydrate). We used a colorimetric method to determine the appearance of the dal fortified with fortificants at different Fe concentrations and under different storage conditions. Relative Fe bioavailability was assessed using an in vitro cell culture bioassay. We found that NaFeEDTA was the most suitable fortificant for red lentil dal, and at 1600 ppm, NaFeEDTA provides 13–14 mg of additional Fe per 100 g of dal. Lentil dal sprayed with fortificant solutions, followed by shaking and drying at 75 °C, performed best with respect to drying time and color change. Total Fe and phytic acid concentrations differed significantly between cooked unfortified and fortified lentil, ranging from 68.7 to 238.5 ppm and 7.2 to 8.0 mg g⁻¹, respectively. The relative Fe bioavailability of cooked fortified lentil was increased by 32.2–36.6% compared to unfortified cooked lentil. We conclude that fortification of lentil dal is effective and could provide significant health benefits to dal-consuming populations vulnerable to Fe deficiency.

QTL mapping of early flowering and resistance to ascochyta blight in chickpea

In western Canada, chickpea (Cicer arietinum L.) production is challenged by short growing seasons and infestations with ascochyta blight. Research was conducted to determine the genetic basis of the association between flowering time and reaction to ascochyta blight in chickpea. Ninety-two chickpea recombinant inbred lines (RILs) developed from a cross between ICCV 96029 and CDC Frontier were evaluated for flowering responses and ascochyta blight reactions in growth chambers and fields at multiple locations and during several years. A wide range of variation was exhibited by the RILs for days to flower, days to maturity, node of first flowering, plant height, and ascochyta blight resistance. Moderate to high broad sense heritability was estimated for ascochyta blight reaction (H(2) = 0.14-0.34) and for days to flowering (H(2) = 0.45-0.87) depending on the environments. Negative correlations were observed among the RILs for days to flowering and ascochyta blight resistance, ranging from r = -0.21 (P < 0.05) to -0.58 (P < 0.0001). A genetic linkage map consisting of eight linkage groups was developed using 349 SNP markers. Seven QTLs for days to flowering were identified that individually explained 9%-44% of the phenotypic variation. Eight QTLs were identified for ascochyta blight resistance that explained phenotypic variation ranging from 10% to 19%. Clusters of QTLs for days to flowering and ascochyta blight resistances were found on chromosome 3 at the interval of 8.6-23.11 cM and on chromosome 8 at the interval of 53.88-62.33 cM.

Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping

Background

Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species’ ability to better withstand abiotic stresses. Genomic resources are scarce for this minor crop species and a better knowledge of the genome-level relationship between these two species would facilitate improvement in both. High-throughput genotyping has facilitated large-scale single nucleotide polymorphism (SNP) identification leading to the development of molecular markers with associated sequence information that can be used to place them in the context of a full genome assembly.

Results

Transcript-based SNPs were identified from six common bean and two tepary bean accessions and a subset were used to generate a 768-SNP Illumina GoldenGate assay for each species. The tepary bean assay was used to assess diversity in wild and cultivated tepary bean and to generate the first gene-based map of the tepary bean genome. Genotypic analyses of the diversity panel showed a clear separation between domesticated and cultivated tepary beans, two distinct groups within the domesticated types, and P. parvifolius was confirmed to be distinct. The genetic map of tepary bean was compared to the common bean genome assembly to demonstrate high levels of collinearity between the two species with differences limited to a few intra-chromosomal rearrangements.

Conclusions

The development of the first set of genomic resources specifically for tepary bean has allowed for greater insight into the structure of this species and its relationship to its agriculturally more prominent relative, common bean. These resources will be helpful in the development of efficient breeding strategies for both species and will facilitate the introgression of agriculturally important traits from one crop into the other.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2499-3) contains supplementary material, which is available to authorized users.

Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Cicer arietinum L.)

Aquaporins (AQPs) are essential membrane proteins that play critical role in the transport of water and many other solutes across cell membranes. In this study, a comprehensive genome-wide analysis identified 40 AQP genes in chickpea (Cicer arietinum L.). A complete overview of the chickpea AQP (CaAQP) gene family is presented, including their chromosomal locations, gene structure, phylogeny, gene duplication, conserved functional motifs, gene expression, and conserved promoter motifs. To understand AQP's evolution, a comparative analysis of chickpea AQPs with AQP orthologs from soybean, Medicago, common bean, and Arabidopsis was performed. The chickpea AQP genes were found on all of the chickpea chromosomes, except chromosome 7, with a maximum of six genes on chromosome 6, and a minimum of one gene on chromosome 5. Gene duplication analysis indicated that the expansion of chickpea AQP gene family might have been due to segmental and tandem duplications. CaAQPs were grouped into four subfamilies including 15 NOD26-like intrinsic proteins (NIPs), 13 tonoplast intrinsic proteins (TIPs), eight plasma membrane intrinsic proteins (PIPs), and four small basic intrinsic proteins (SIPs) based on sequence similarities and phylogenetic position. Gene structure analysis revealed a highly conserved exon-intron pattern within CaAQP subfamilies supporting the CaAQP family classification. Functional prediction based on conserved Ar/R selectivity filters, Froger's residues, and specificity-determining positions suggested wide differences in substrate specificity among the subfamilies of CaAQPs. Expression analysis of the AQP genes indicated that some of the genes are tissue-specific, whereas few other AQP genes showed differential expression in response to biotic and abiotic stresses. Promoter profiling of CaAQP genes for conserved cis-acting regulatory elements revealed enrichment of cis-elements involved in circadian control, light response, defense and stress responsiveness reflecting their varying pattern of gene expression and potential involvement in biotic and abiotic stress responses. The current study presents the first detailed genome-wide analysis of the AQP gene family in chickpea and provides valuable information for further functional analysis to infer the role of AQP in the adaptation of chickpea in diverse environmental conditions.

Identification and Expression Analysis of Candidate Genes Involved in Carotenoid Biosynthesis in Chickpea Seeds

Plant carotenoids have a key role in preventing various diseases in human because of their antioxidant and provitamin A properties. Chickpea is a good source of carotenoid among legumes and its diverse germplasm and genome accessibility makes it a good model for carotenogenesis studies. The structure, location, and copy numbers of genes involved in carotenoid biosynthesis were retrieved from the chickpea genome. The majority of the single nucleotide polymorphism (SNPs) within these genes across five diverse chickpea cultivars was synonymous mutation. We examined the expression of the carotenogenesis genes and their association with carotenoid concentration at different seed development stages of five chickpea cultivars. Total carotenoid concentration ranged from 22 μg g^-1 in yellow cotyledon kabuli to 44 μg g^-1 in green cotyledon desi at 32 days post anthesis (DPA). The majority of carotenoids in chickpea seeds consists of lutein and zeaxanthin. The expression of the selected 19 genes involved in carotenoid biosynthesis pathway showed common pattern across five cultivars with higher expression at 8 and/or 16 DPA then dropped considerably at 24 and 32 DPA. Almost all genes were up-regulated in CDC Jade cultivar. Correlation analysis between gene expression and carotenoid concentration showed that the genes involved in the primary step of carotenoid biosynthesis pathway including carotenoid desaturase and isomerase positively correlated with various carotenoid components in chickpea seeds. A negative correlation was found between hydroxylation activity and provitamin A concentration in the seeds. The highest provitamin A concentration including β-carotene and β-cryptoxanthin were found in green cotyledon chickpea cultivars.

Fine mapping for double podding gene in chickpea

For the first time, fine mapping for sfl locus was carried out using a battery of new STMS and SNP markers. The target region was delimited to 92.6 Kb where seven annotated genes were found that could be candidate genes for the simple/double podding trait in chickpea. Four recombinant inbred populations (RIP-1, RIP-7, RIP-11, and CPR-01) were used to map the double podding gene (sfl) in chickpea. In RIP-1, the gene was initially mapped on linkage group (LG) 6 between the two sequence-tagged microsatellite site (STMS) markers TA120 and TR1. Eight new STMS markers were added onto LG6 in the target region and sfl locus was finally located between CAGM27819 and CAGM27777 markers within an interval of 2 cM. Seven out of the eight markers were mapped in RIP-7 and its reciprocal RIP-11 confirming the location of the sfl locus to a 4.8 cM interval flanked by TR44 and CAGM27705. Furthermore, using a high-density single nucleotide polymorphism (SNP) map of CPR-01, sfl was mapped to the same genomic region in a 5.1 cM interval between TR44 and the SNP scaffold1646p97220. Five pairs of near isogenic lines (NILs) and eight recombinant inbred lines (RILs) were used to refine this region in the chickpea physical map. Combining data from linkage analysis in four RIPs, marker physical positions and recombination events obtained in both pairs of NILs and selected RILs, sfl could be placed within a genomic window of 92.6 Kb. Seven annotated genes were extracted from this region. The regulator of axillary meristem-predicted gene could be a candidate gene for the simple/double podding gene. This study provides additional set of markers flanking and tightly linked to sfl locus that are useful for marker-assisted selection.

Genetic diversity and association mapping of iron and zinc concentrations in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is the world's second most important pulse crop after common bean. Chickpea has historically been an important daily staple in the diet of millions of people, especially in the developing countries. Current chickpea breeding programs have mainly been directed toward high yield, biotic and abiotic stress resilience that has increased global production, but less attention has been directed toward improving micronutrient concentrations in seeds. In an effort to develop micronutrient-dense chickpea lines, a study to examine the variability and to identify SNP alleles associated with seed iron and zinc concentrations was conducted using 94 diverse accessions of chickpea. The results indicated that there is substantial variability present in chickpea germplasm for seed iron and zinc concentrations. In the current set of germplasm, zinc is negatively correlated with grain yield across all locations and years; whereas the negative correlation between iron and grain yield was only significant at the Elrose locality. Eight SNP loci associated with iron and (or) zinc concentrations in chickpea seeds were identified. One SNP located on chromosome 1 (chr1) is associated with both iron and zinc concentrations. On chr4, three SNPs associated with zinc concentration and two SNPs for iron concentration were identified. Two additional SNP loci, one on chr6 and the other on chr7, were also found to be associated with iron and zinc concentrations, respectively. The results show potential opportunity for molecular breeding for improvement of seed iron and zinc concentrations in chickpea.

Genotype-specific variation in the structure of root fungal communities is related to chickpea plant productivity

Increasing evidence supports the existence of variations in the association of plant roots with symbiotic fungi that can improve plant growth and inhibit pathogens. However, it is unclear whether intraspecific variations in the symbiosis exist among plant cultivars and if they can be used to improve crop productivity. In this study, we determined genotype-specific variations in the association of chickpea roots with soil fungal communities and evaluated the effect of root mycota on crop productivity. A 2-year field experiment was conducted in southwestern Saskatchewan, the central zone of the chickpea growing region of the Canadian prairie. The effects of 13 cultivars of chickpea, comprising a wide range of phenotypes and genotypes, were tested on the structure of root-associated fungal communities based on internal transcribed spacer (ITS) and 18S rRNA gene markers using 454 amplicon pyrosequencing. Chickpea cultivar significantly influenced the structure of the root fungal community. The magnitude of the effect varied with the genotypes evaluated, and effects were consistent across years. For example, the roots of CDC Corrine, CDC Cory, and CDC Anna hosted the highest fungal diversity and CDC Alma and CDC Xena the lowest. Fusarium sp. was dominant in chickpea roots but was less abundant in CDC Corrine than the other cultivars. A bioassay showed that certain of these fungal taxa, including Fusarium species, can reduce the productivity of chickpea, whereas Trichoderma harzianum can increase chickpea productivity. The large variation in the profile of chickpea root mycota, which included growth-promoting and -inhibiting species, supports the possibility of improving the productivity of chickpea by improving its root mycota in chickpea genetic improvement programs using traditional breeding techniques.

Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly

BACKGROUND

In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly.

RESULTS

Genic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins and 732 SNPs from Illumina GoldenGate assay. The map covered 653 cM of the chickpea genome with an average distance between adjacent markers of 0.5 cM. To date, this is the most extensive genetic map of chickpea using an intraspecific population. The alignment of the map with the CDC Frontier genome assembly revealed an overall conserved marker order; however, a few local inconsistencies within the Cicer arietinum pseudochromosome 1 (Ca1), Ca5 and Ca8 were detected. The map enabled the alignment of 215 unplaced scaffolds from the CDC Frontier draft genome assembly. The alignment also revealed varying degrees of recombination rates and hotspots across the chickpea genome.

CONCLUSIONS

A high-density genetic map using RAD-Seq GBS and Illumina GoldenGate assay was developed and aligned with the existing kabuli chickpea draft genome sequence. The analysis revealed an overall conserved marker order, although some localized inversions between draft genome assembly and the genetic map were detected. The current analysis provides an insight of the recombination rates and hotspots across the chickpea genome.

Genetic characterization of the acetohydroxyacid synthase (AHAS) gene responsible for resistance to imidazolinone in chickpea (Cicer arietinum L.)

A point mutation in the AHAS1 gene leading to resistance to imidazolinone in chickpea was identified. The resistance is inherited as a single gene. A KASP marker targeting the mutation was developed. Weed control in chickpea (Cicer arietinum L.) is challenging due to poor crop competition ability and limited herbicide options. A chickpea genotype with resistance to imidazolinone (IMI) herbicides has been identified, but the genetic inheritance and the mechanism were unknown. In many plant species, resistance to IMI is caused by point mutation(s) in the acetohydroxyacid synthase (AHAS) gene resulting in an amino acid substitution preventing herbicide attachment to the molecule. The main objective of this research was to characterize the resistance to IMI herbicides in chickpea. Two homologous AHAS genes namely AHAS1 and AHAS2 sharing 80 % amino acid sequence similarity were identified in the chickpea genome. Cluster analysis indicated independent grouping of AHAS1 and AHAS2 across legume species. A point mutation in the AHAS1 gene at C675 to T675 resulting in an amino acid substitution from Ala205 to Val205 confers the resistance to IMI in chickpea. A KASP marker targeting the point mutation was developed and effectively predicted the response to IMI herbicides in a recombinant inbred (RI) population of chickpea. The RI population was used in molecular mapping where the major locus for the reaction to IMI herbicide was mapped to chromosome 5. Segregation analysis across an F2 population and RI population demonstrated that the resistance is inherited as a single gene in a semi-dominant fashion. The simple genetic inheritance and the availability of KASP marker generated in this study would speed up development of chickpea varieties with resistance to IMI herbicides.

Genetic control and identification of QTLs associated with visual quality traits of field pea (Pisum sativum L.)

Visual quality of field pea (Pisum sativum L.) is one of the most important determinants of the market value of the harvested crop. Seed coat color, seed shape, and seed dimpling are the major components of visual seed quality of field pea and are considered as important breeding objectives. The objectives of this research were to study the genetics and to identify quantitative trait loci (QTLs) associated with seed coat color, seed shape, and seed dimpling of green and yellow field peas. Two recombinant inbred line populations (RILs) consisting of 120 and 90 lines of F(5)-derived F(7) (F(5:7)) yellow pea (P. sativum 'Alfetta' × P. sativum 'CDC Bronco') and green pea (P. sativum 'Orb' × P. sativum 'CDC Striker'), respectively, were evaluated over two years at two locations in Saskatchewan, Canada. Quantitative inheritance with polygenic control and transgressive segregation were observed for all visual quality traits studied. All 90 RILs of the green pea population and 92 selected RILs from the yellow pea population were screened using AFLP and SSR markers and two linkage maps were developed. Nine QTLs controlling yellow seed lightness, 3 for yellow seed greenness, 15 for seed shape, and 9 for seed dimpling were detected. Among them, five QTLs located on LG II, LG IV, and LG VII were consistent in at least two environments. The QTLs and their associated markers will be useful tools to assist pea breeding programs attempting to pyramid positive alleles for the traits.

Genetic control and QTL analysis of cotyledon bleaching resistance in green field pea (Pisum sativum L.)

Resistance to bleaching is an important factor for quality grading of Canadian green field pea and an important selection criterion in green pea improvement. This research was conducted to determine the genetic control of bleaching resistance in green peas using 90 recombinant inbred lines (RILs) derived from a cross between cultivars Orb and CDC Striker. These lines were evaluated under field conditions for two years in two locations in Saskatchewan, Canada. Harvested whole seeds and cotyledons were evaluated for greenness using the Hunter Lab colorimeter before and after exposure to a high light intensity accelerated bleaching treatment. The RILs were genotyped using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) molecular markers. Heritability estimates for whole seed and cotyledon greenness were moderate (0.72 and 0.69, respectively) and increased when assessed after exposing whole seeds and cotyledons to accelerated bleaching conditions (0.83 and 0.82, respectively). The genetic linkage map constructed based on a total of 224 AFLP and SSR markers spanned over 890 cM of the pea genome. Multiple QTL mapping detected major QTLs on LG IV and LG V as well as location- and year-specific QTLs on LG II and LG III associated with green cotyledon bleaching resistance in field pea. The results demonstrated the importance of the seed coat in protecting the cotyledons from bleaching.

Genetic mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.) using a simple sequence repeat linkage map

Ascochyta blight, caused by the fungus Ascochyta rabiei (Pass.) Lab., is one of the most devastating diseases of chickpea (Cicer arietinum L.) worldwide. Research was conducted to map genetic factors for resistance to ascochyta blight using a linkage map constructed with 144 simple sequence repeat markers and 1 morphological marker (fc, flower colour). Stem cutting was used to vegetatively propagate 186 F2 plants derived from a cross between Cicer arietinum L. 'ICCV96029' and 'CDC Frontier'. A total of 556 cutting-derived plants were evaluated for their reaction to ascochyta blight under controlled conditions. Disease reaction of the F1 and F2 plants demonstrated that the resistance was dominantly inherited. A Fain's test based on the means and variances of the ascochyta blight reaction of the F3 families showed that a few genes were segregating in the population. Composite interval mapping identified 3 genomic regions that were associated with the reaction to ascochyta blight. One quantitative trait locus (QTL) on each of LG3, LG4, and LG6 accounted for 13%, 29%, and 12%, respectively, of the total estimated phenotypic variation for the reaction to ascochyta blight. Together, these loci controlled 56% of the total estimated phenotypic variation. The QTL on LG4 and LG6 were in common with the previously reported QTL for ascochyta blight resistance, whereas the QTL on LG3 was unique to the current population.

Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters

Random amplified polymorphic DNA, simple sequence repeat, and inter-simple sequence repeat markers were used to estimate the genetic relations among 65 pea varieties (Pisum sativum L.) and 21 accessions from wild Pisum subspecies (subsp.) abyssinicum, asiaticum, elatius, transcaucasicum, and var. arvense. Fifty-one of these varieties are currently available for growers in western Canada. Nei and Li's genetic similarity (GS) estimates calculated using the marker data showed that pair-wise comparison values among the 65 varieties ranged from 0.34 to 1.00. GS analysis on varieties grouped according to their originating breeding programs demonstrated that different levels of diversity were maintained at different breeding programs. Unweighted pair-group method arithmetic average cluster analysis and principal coordinate analysis on the marker-based GS grouped the cultivated varieties separately from the wild accessions. The majority of the food and feed varieties were grouped separately from the silage and specialty varieties, regardless of the originating breeding programs. The analysis also revealed some genetically distinct varieties such as Croma, CDC Handel, 1096M-8, and CDC Acer. The relations among the cultivated varieties, as revealed by molecular-marker-based GS, were not significantly correlated with those based on the agronomic characters, suggesting that the 2 systems give different estimates of genetic relations among the varieties. However, on a smaller scale, a consistent subcluster of genotypes was identified on the basis of agronomic characters and their marker-based GS. Furthermore, a number of variety-specific markers were identified in the current study, which could be useful for variety identification. Breeding strategies to maintain or enhance the genetic diversity of future varieties are proposed.

Quantitative trait loci for lodging resistance, plant height and partial resistance to mycosphaerella blight in field pea (Pisum sativum L.)

With the development of genetic maps and the identification of the most-likely positions of quantitative trait loci (QTLs) on these maps, molecular markers for lodging resistance can be identified. Consequently, marker-assisted selection (MAS) has the potential to improve the efficiency of selection for lodging resistance in a breeding program. This study was conducted to identify genetic loci associated with lodging resistance, plant height and reaction to mycosphaerella blight in pea. A population consisting of 88 recombinant inbred lines (RILs) was developed from a cross between Carneval and MP1401. The RILs were evaluated in 11 environments across the provinces of Manitoba, Saskatchewan and Alberta, Canada in 1998, 1999 and 2000. One hundred and ninety two amplified fragment length polymorphism (AFLP) markers, 13 random amplified polymorphic DNA (RAPD) markers and one sequence tagged site (STS) marker were assigned to ten linkage groups (LGs) that covered 1,274 centi Morgans (cM) of the pea genome. Six of these LGs were aligned with the previous pea map. Two QTLs were identified for lodging resistance that collectively explained 58% of the total phenotypic variation in the mean environment. Three QTLs were identified each for plant height and resistance to mycosphaerella blight, which accounted for 65% and 36% of the total phenotypic variation, respectively, in the mean environment. These QTLs were relatively consistent across environments. The AFLP marker that was associated with the major locus for lodging resistance was converted into the sequence-characterized amplified-region (SCAR) marker. The presence or absence of the SCAR marker corresponded well with the lodging reaction of 50 commercial pea varieties.

Mapping genetic factors affecting the reaction to Xanthomonas axonopodis pv. phaseoli in Phaseolus vulgaris L. under field conditions

The objectives of the present study were to evaluate the field effects of Xanthomonas axonopodis pv. phaseoli (Xap), which causes common bacterial blight (CBB) on common bean (Phaseolus vulgaris L.), and to identify genetic factors for resistance to CBB using a linkage map constructed with random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), simple sequence repeat (SSR), and amplified fragment length polymorphism (AFLP) markers. One hundred and forty-two F2:4 lines, derived from a cross between 'OAC Seaforth' and 'OAC 95-4', and the parents were evaluated for their field reaction to CBB. In the inoculated plots, the reaction to CBB was negatively correlated with seed yield, days to maturity, plant height, hypocotyl diameter, pods per plant, and harvest index. A reduction in seed yield and its components was observed when disease-free and CBB-inoculated plots were compared. The broad-sense heritability estimate of the reaction to CBB was 0.74. The disease segregation ratio was not significantly different from the expected segregation ratio for a single locus in an F2 generation. The major gene for CBB resistance was localized on linkage group (LG) G5. A simple interval mapping procedure identified three genomic regions associated with the reaction to CBB. One quantitative trait loci (QTL), each on LG G2 (BNG71DraI), G3 (BNG21EcoRV), and G5 (PHVPVPK-1) explained 36.3%, 10.2%, and 42.2% of the phenotypic variation for the reaction to CBB, respectively. Together, these loci explained 68.4% of the phenotypic variation. The relative positions of these QTL on the core common bean map and their comparison with the previous QTL for CBB resistance are discussed.Key words: common bean, molecular markers, common bacterial blight.