Assessment of phenotypic and genetic variation against pod borer among a subset of elite pigeonpea (Cajanus cajan) genotypes in Kenya

Molecular marker information supported by quality morphological data facilitates the choice of suitable parents for applied breeding. The main aim of this study was to assess genetic diversity among 55 cultivated yield elite pigeonpea lines using 21 simple sequence repeat (SSR) markers that are well distributed across the genome. Among the 55 pigeonpea genotypes, 16 medium duration were selected and evaluated in the field for response to pod borer resistance in varied agro-ecological zones of Kenya during long rains of April-October cropping season Twenty one primer pairs detected 80 alleles with a mean of 3.9 alleles per locus and polymorphism information content (PIC) ranging from 0.09 to 0.75 averaging to 0.39 suggesting a low genetic diversity. However, marker CcM1820 revealed the highest number of alleles (9) with a PIC value of 0.75. The genotype response to pod borer attack was significant (P≤0.05) with three genotypes (ICEAPs 01541, 01154-2 and 00902) revealing tolerance to pod borer. The markers based on Neighbor Joining, grouped the 55 genotypes into three main clusters based on parentage selection. Most genotypes developed from ICEAP 00068 as the maternal parent were grouped in Cluster I while cluster II comprised of improved genotypes and cluster III comprised genotypes developed from ICPL 87091 as maternal parent. The resistant genotypes identified in the field experiment were grouped in cluster I except ICEAP 00902 which grouped in cluster II. Future studies should focus on broadening genetic base by including more landraces and wild relatives to maximize selection and improve breeding work

Study of root traits of chickpea (Cicer arietinum L.) under drought stress

Roots are among the first defence towards drought with other morpho-physiological and biochemical mechanisms employed by plants. To understand precisely the root traits contribution towards yield, parental chickpea genotypes with well known drought response were field evaluated under drought and optimal irrigation in rain-out shelter. A total of ten genotypes planted in 1.2 m PVC lysimeters were subjected to three water stress levels: high moisture stress, medium water stress, and low water stresses. Root traits, such as root length density, total root dry weight, root dry weight and root: shoot ratio, were measured at 40 days after sowing. The roots were washed and scanned using WinRHIZO software. The ANOVA showed that there was significant difference (P < 0.05) in traits measured amongst test genotypes which included shoot biomass, root biomass, total root length (RL) and root length density (RLD). The results also showed that there were significant variations (P < 0.05) in water regimes and traits decreased with increasing moisture stress from low to high moisture regime. Furthermore, there were variations in root anatomy between the two major chickpea types where majority of the best performing genotypes under low moisture regimes were of the Desi type (e.g. ICC 4958, ICCV 00108, ICCV 92944 and ICCV 92318) as compared to Kabulis which had better and higher response under high moisture regime in this study. These traits could be used for indirect selection for drought tolerance especially in early stages of breeding for drought tolerance which would consequently reduce the cost of multi-location field evaluation in the breeding programs

Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs

Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively. © 2014 Saxena et al

Effect of Drought Stress on Yield Performance of Parental Chickpea Genotypes in Semi-arid Tropics

Chickpea (Cicer arietinum L.) is an important cool season food legumes with indeterminate growth habit. The crop is valued for its nutritive seeds and used as animal feed in many developing countries. The productivity of the crop is constrained by several abiotic stresses, among which drought stress is one of the key determinants of crop performance aaccounting for 40-50% yield reduction globally. The present study was conducted to screen, evaluate and select chickpea genotypes possessing high yield potential under drought stress condition at ASALs (arid and semi-arid lands) of Kenya. The experiment was conducted at Chemeron dry land and Eco-tourism Research station, Egerton University and Kenya Agricultural and Livestock Research Institute (KALRO), Pekerra, Marigat, Baringo County. The genotypes were planted in RCBD (randomized complete block design) in three replicates at a spacing of 30 cm × 10 cm, giving a plant density of approximately 25 plants/m2. Combined analysis of variance revealed existence of highly significant differences among the tested genotypes for most of the agronomic traits. Overall, the highest grain yield was obtained from ICCV 92944 (1,173 kg/ha), ICCV 92318 (1,103 kg/ha) and CAVIR (975 kg/ha), ICCV 92318 (967 kg/ha), ICCV 00108 (956 kg/ha) and ICC 4958 (921 kg/ha): possibly due to its comparatively higher drought (and heat) tolerance, and hence could be used as sources of drought tolerance in further breeding programs. This study was carried out in few drought tolerant sites and further more sites need to be evaluated in addition to other drought and heat screening and optimization of protocols, facilities and analytical approaches to identify better genotypes that respond appropriately to climate change

Marker assisted backcross breeding to enhance drought tolerance in Kenyan chickpea (Cicer arietinum L.) germplasm

Drought is the number one constraint in chickpea production. In the past, breeding efforts to improve terminal drought tolerance have been hindered by its quantitative genetic basis and poor understanding of the physiological basis of yield in water-limited conditions

Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1–7 seasons and 1–3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance

Evaluation of Genotype x Environment Interaction and Stability of Grain Yield and Related Yield Components in Pearl Millet (Pennisetum glaucum (L.) R.Br.)

Thirty six pearl millet genotypes were evaluated in randomized complete block design with two replications during 2011/2012 at two locations to study the magnitude of genotype by environment interaction for yield and yield related traits and identify the most stable high yielding genotypes. ANOVA of data at individual locations revealed significant differences among genotypes at Marigat and Koibatek for all yield components. Combined mean analysis of variance showed that the Genotype and location main effects and the genotype by environment interaction were highly significant (P≤0.01) for grain yield and other traits, indicating differential response of genotypes across testing locations and the need for stability analysis. Marigat was the most suitable environment and gave highest mean grain yield of 3620 kg/ha. The lowest yield 870 Kg/ha was recorded at Koibatek. Genotypes EUP 32, EUP 35, EUP 19 and EUP 10 produced high mean yield of 3530, 3080, 2690 and 2590 kg/ha respectively. The lowest grain 1290 kg/ha was obtained from genotype EUP 4.Based on the parameters of stability, three stable (widely adapted) and high yielding genotypes (EUP 34, EUP 18, and EUP 9) were identified. They also out-yield the standard open pollinated variety (OPV) check, Kat PM2. Genotypes EUP 32 was the highest yielding across all sites followed by EUP 35 and could be recommended for further multi-location evaluation in warmer environment and possible release for commercial production. The findings of this study showed that pearl millet hybrids have high potential for commercial production in Kenya than the OPVs. The ANOVA results showed that the effects of environments, genotypes and genotype x environment interaction (GE) were important in trait expression and performance of genotypes. In addition, it was observed that amount of rainfall received at both vegetative and post-anthesis phases and temperature had an effect on grain yield. The GGE biplot analysis characterised the environments in terms of stability and productivity, where Marigat was the best for grain yield; implying that environment-specific selection should be adopted. Genotypes EUP 34, EUP 18, and EUP 9 were the best performing since they out yielded the standard OPV check. These stable high yielding genotypes can be evaluated further in varied agro-ecologies and recommended for release as commercial hybrid varieties in ASALs of Kenya

Performance of marker assisted backcross breeding (MABC) elite chickpea lines under drought conditions in Kenya

Drought is the most important constraint affecting production of chickpea and other crops as well. Quantitative traits like drought tolerance are multigenic and their inheritance is difficult to predict hence the need to explore more precise breeding techniques like maker assisted selection. The aim of this study was to introgress the identified root trait QTLs into Kenyan adapted cultivar to enhance drought tolerance through marker assisted backcrossing. Four varieties Chania Desi 1 (ICCV 97105), ICCV10, ICCV 92318, and Saina K1 (ICCV 95423) were selected as a recurrent parents for improvement among ten agronomically superior elite cultivars after exhibiting high polymorphism with SSR markers. Five molecular markers (CaM1903, CaM1502, TAA 170, NCPGR21 and GA11) were validated for use in MABC deployed in this study. Crosses were made between the four parents and ICC 4958 followed by marker screening of the F1 seedling progenies for the QTL of interest. Identified true heterozygotes were used as donors and backcrossed to the recurrent parent to obtain BC1F1 seeds. The process was repeated to obtain BC2F1 and finally BC3F1 with molecular marker identification of seedlings carrying the QTL region at each step. Results of evaluation in one trial site in Kenya semi-arid area (Koibatek ATC) of MABC lines for the four parents ICCV10 (24 lines), ICCV 92318 (8lines), ICCV 97105 (12 lines) and Saina K1-ICCV 95423 (10 lines) showed that the best progenies with higher levels of drought resistance and yield were ICCMABCD-21, 9, 20, 23, 15, 22, 5, 14, 16, 19 and 6 with yields > 2.5 tons/ha. The results indicated that it is possible to transfer QTL that confers drought tolerance using MABC. The best progenies are undergoing further evaluation to validate the contribution of the introgressed QTL in improving drought tolerance and yield

Introgression of drought tolerance traits into adapted Kenyan chickpea varieties using marker assisted backcrossing (MABC)

Drought is the major constraint causing considerable yield reduction in chickpea. Roots play a critical role in enhancing drought tolerance. The main objective of the study was to introgress drought tolerant root traits into Kenyan chickpea varieties through marker assisted breeding (MABC). Eight simple sequence repeat (SSR) markers, linked to quantitative trait loci (QTL) for root and yield traits, were used to screen the parents at ICRISAT, India. In addition, 1144 single nucleotide polymorphic markers (SNPs) were also used in genotyping these parents at Legume Genomics Center, United Kingdom. Crosses were made between two selected varieties, ICCV 92944 (Chania Desi II) and ICCV 00108 (LDT 068) and ‘QTL-hotspot’ donor parent ICC 4958 that has extensive rooting system. Polymor- In the face of increasing water scarcity, breeding for higher transpiration efficiency (TE), that is, the biomass produced per unit of water transpired, has become crucial. This could be achieved by reducing plant transpiration through a better closure of the stomatal pores at the leaf surface. However, this strategy generally also lowers growth, as stomatal opening is necessary for the capture of atmospheric CO2 that feeds daytime photosynthesis. Here, we considered the reduction in transpiration rate at night (En), when photosynthesis is inactive, as a possible strategy to limit water use without altering growth. We carried out a genetic analysis for En and TE in grapevine, a major crop in drought-prone areas. A 3 year experiment was conducted on the F1 progeny from a cross between Syrah and Grenache cultiphic SSR and SNP markers were used to select progenies with root QTL at F1, BC1F1 and BC2F1 that were later advanced to BC2F3. The BC2F3 populations were evaluated for root traits at Egerton University in randomized complete block design with two replications in pot experiment. The BC2F3 families were significantly different for root dry weight (RDW), shoot dry weight (SDW), total plant dry weight (PDW) and root to shoot dry weight (R/S) ratio (R/S) for Chania Desi II x ICC 4958 and R/S for LDT 068 x ICC 4958. These lineshad significantly improved root traits compared the recurrent parents. MABC is aneffective and efficient method of introgressing complex drought tolerant traits which leads to improvement in yield especially under drought conditions

Evaluation of Selected Pigeonpea (Cajanus cajan (L.) Millsp.) Genotypes for Resistance to Insect Pest Complex in Dry Areas of North Rift Valley, Kenya

Pigeonpea is an important pulse crop that has gained importance in semi-arid tropics, although its yield potential has not been fully realized due to biotic and abiotic stresses that limit its production. Insect pest complex of pod borer (Helicoverpa armigera), sucking bug (Clavigralla tomentosicollis) and pod fly (Melanagromyza cholcosoma) are the major limiting factors to its production causing up to 100% yield loss. The objective of this study was to evaluate resistant genotypes to insect pest complex in dry parts of North Rift Valley Kenya. The study was carried out in three sites (Kenya Agricultural Livestock Research Organization- Marigat, Agricultural Training Centre-Koibatek and Fluorspar-Chepsirei) for one season during long rain of April-November 2014 growing season. Sixteen ICRISAT elite genotypes were evaluated in randomized complete block design (RCBD) with 75cm inter and 25 cm intra spacing. Significant (P≤0.05) differences in grain yield performance, incidence and severity of the insect pests were revealed in all sites. The damage was more severe in Marigat (Pod borer-37.2%, Sucking bug-39.3% and pod fly-5.9%) than ATC- Koibatek (Pod borer-1.9%, Sucking bug-8.4% and pod fly-5.9%) and Fluorspar (Pod borer-3.6%, Sucking bug-6.8% and pod fly-2.9%). Genotypes ICEAPs 00850R, 00902, 01541 and 1154-2 showed potential levels of resistance to the insect pest complex and high yields. Grain yield associated negatively (P≤0.05) with pod borer and sucking bug damage correlated non-significantly with pod fly damage. The potential genotypes identified in this study need to be further evaluated in two seasons and in other multi-locations to validate these findings to be used in breeding