Variation in important seed constituents among various chickpea genotypes

Chickpea (Cicer arietinum L.) is the third most important pulse crop and an excellent source of protein in the human diet (Garg et al., 2011). However, the presence of anti-nutritional factors like the raffinose family oligosaccharides (RFO) restrains its acceptability as food and feed (Olmedilla Alonso et al., 2010). Higher concentration of RFO in chickpea seeds affects human health negatively and plays an important physiological role in plants (Martinez-Villaluenga et al., 2008). Hence, there is a need to reduce RFO concentration in seeds without affecting plant growth. To achieve this objective, it is imperative to understand the biochemical mechanism and genetic basis of the RFO biosynthetic pathway. As a first step, we studied the variation in RFO concentration along with starch and protein in a germplasm collection of 152 genotypes. These genotypes were grown in the field for two consecutive years 2009 and 2010 at ICRISAT in India and in greenhouse in 2010 at the University of Saskatchewan, Canada. Enzymatic methods using commercial kits (Megazyme International) were used to determine starch and total RFO concentration. Protein concentration was determined by FP-528 Protein/Nitrogen Analyzer (Leco). To determine individual RFO profiles, we have developed a new high performance anion exchanged chromatography based gradient method. Results showed that lentil genotypes from greenhouse cultivation had significantly lower (1.58–4.67 mmoles/100 g-1) concentration of total RFO than that of their field grown counterparts. Stachyose was identified as a major RFO in chickpea seeds followed by raffinose and verbascose. Individual RFOs (raffinose, stachyose and verbascose) showed higher concentration in the ICRISAT 2009 set than that of the ICRiSAT 2010 and greenhouse sets. An obvious strong positive correlation was found among total RFO and individual members of the family. Starch concentration in chickpea genotypes ranged from 25.7 to 50.7% of total seed weight. ICRISAT 2009 set (29.4–50.7%) had a higher amount of starch than that in ICRISAT 2010 (25.7–44.5%) and the greenhouse set (28.2–44.4%). Starch concentration showed a positive correlation with total RFO. The chickpea seeds have 13.5–31.7% protein. Genotypes in the ICRISAT 2010 set had a higher amount of protein (17.92–31.73%) compared to the ICRISAT 2009 and greenhouse sets. A significant negative correlation was observed between protein and starch concentration. Analysis of variance revealed a significant effect (P < 0.001) of genotype, environment and genotype x environment on chickpea seed constituents. This study has revealed the RFO variation in chickpea genotypes and its correlation with other important seed constituents. These findings will be helpful in genotype screening for contrasting RFO concentration and in exploring the RFO biosynthetic pathway

Construction of a genetic linkage map and QTL analysis for late leaf spot and rust in groundnut (Arachis hypogaea L.)

Late Leaf Spot (Phaeoisariopsis personata [(Berk. and Curt.) Deighton] and rust (Puccinia arachidis Speg.) are the major foliar diseases of groundnut that often occur together leading to 50-70% yield loss in the crop. Two hundred and sixty eight RILs (TAG 24 × GPBD 4) segregating for late leaf spot (LLS) and rust were used to undertake QTL analysis. Phenotyping of the population was carried out under artificial disease epiphytotics for three seasons. Positive correlations between different stages, high to very high heritability and independent nature of inheritance between both the diseases was observed. Parental genotypes (TAG 24 and GPBD 4) were screened with 1089 SSR markers, of which 67 (6.15%) were found polymorphic. The study yielded partial linkage map with 14 linkage groups integrating 56 SSR markers with 364.40 cM genome coverage and average marker distance of 8.7cM. Composite interval mapping (CIM) showed 12 QTLs for LLS (1.2 to 5.6%) in three different environments. In case of rust, 13 QTLs were detected in three different environments with phenotypic variance ranged upto 54.4%. Furthermore, a major QTL associated with rust was identified by both CIM and single marker analysis (SMA) that contribute 18.4 to 54.4% phenotypic variance. Markers linked with this QTL are being validated using a wide range of resistant / susceptible breeding lines as well as progeny lines of another mapping population (TG 26 × GPBD 4). SSR marker(s) linked with major QTL for rust, once validated, will be the potential marker(s) for undertaking molecular breeding for rust resistance

Genetic enhancement of resistance to foliar diseases

Rust and Late leaf spot are among the most destructive and widespread diseases of groundnut. Cultivation of resistant varieties is economically most viable and environmentally sound strategy. Germplasm with high level of resistance is available in cultivated and/or related wild species. In spite of innumerable attempts, breeding has met with limited success in combining resistance with yield, crop quality and adaptation. The modern tool of Marker Assisted Selection (MAS) is expected to improve the speed and precision of resistance breeding. The progress and challenges in the application of molecular markers in breeding for resistance to foliar diseases will be discussed

The GCP molecular marker toolkit, an instrument for use in breeding food security crops

Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access, particularly those in developing countries. This situation separates them from developed countries, which have better endowed programs for developing varieties. To close this growing knowledge gap, we conducted an intensive literature review and consulted with more than 150 crop experts on the use of molecular markers in the breeding program of 19 food security crops. The result was a list of effectively used and highly reproducible sequence tagged site (STS), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), and sequence characterized amplified region (SCAR) markers. However, only 12 food crops had molecular markers suitable for improvement. That is, marker-assisted selection is not yet used for Musa spp., coconut, lentils, millets, pigeonpea, sweet potato, and yam. For the other 12 crops, 214 molecular markers were found to be effectively used in association with 74 different traits. Results were compiled as the GCP Molecular Marker Toolkit, a free online tool that aims to promote the adoption of molecular approaches in breeding activities

A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.)

Late leaf spot (LLS) and rust are two major foliar diseases of groundnut (Arachis hypogaea L.) that often occur together leading to 50–70% yield loss in the crop. A total of 268 recombinant inbred lines of a mapping population TAG 24 × GPBD 4 segregating for LLS and rust were used to undertake quantitative trait locus (QTL) analysis. Phenotyping of the population was carried out under artificial disease epiphytotics. Positive correlations between different stages, high to very high heritability and independent nature of inheritance between both the diseases were observed. Parental genotypes were screened with 1,089 simple sequence repeat (SSR) markers, of which 67 (6.15%) were found polymorphic. Segregation data obtained for these markers facilitated development of partial linkage map (14 linkage groups) with 56 SSR loci. Composite interval mapping (CIM) undertaken on genotyping and phenotyping data yielded 11 QTLs for LLS (explaining 1.70–6.50% phenotypic variation) in three environments and 12 QTLs for rust (explaining 1.70–55.20% phenotypic variation). Interestingly a major QTL associated with rust (QTLrust01), contributing 6.90–55.20% variation, was identified by both CIM and single marker analysis (SMA). A candidate SSR marker (IPAHM 103) linked with this QTL was validated using a wide range of resistant/susceptible breeding lines as well as progeny lines of another mapping population (TG 26 × GPBD 4). Therefore, this marker should be useful for introgressing the major QTL for rust in desired lines/varieties of groundnut through marker-assisted backcrossing

Genetics, genomics and breeding of groundnut (Arachis hypogaea L.)

Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker‐assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties