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

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

Two decades of association mapping: Insights on disease resistance in major crops

Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding

Mutation of the Zebrafish Nucleoporin elys Sensitizes Tissue Progenitors to Replication Stress

The recessive lethal mutation flotte lotte (flo) disrupts development of the zebrafish digestive system and other tissues. We show that flo encodes the ortholog of Mel-28/Elys, a highly conserved gene that has been shown to be required for nuclear integrity in worms and nuclear pore complex (NPC) assembly in amphibian and mammalian cells. Maternal elys expression sustains zebrafish flo mutants to larval stages when cells in proliferative tissues that lack nuclear pores undergo cell cycle arrest and apoptosis. p53 mutation rescues apoptosis in the flo retina and optic tectum, but not in the intestine, where the checkpoint kinase Chk2 is activated. Chk2 inhibition and replication stress induced by DNA synthesis inhibitors were lethal to flo larvae. By contrast, flo mutants were not sensitized to agents that cause DNA double strand breaks, thus showing that loss of Elys disrupts responses to selected replication inhibitors. Elys binds Mcm2-7 complexes derived from Xenopus egg extracts. Mutation of elys reduced chromatin binding of Mcm2, but not binding of Mcm3 or Mcm4 in the flo intestine. These in vivo data indicate a role for Elys in Mcm2-chromatin interactions. Furthermore, they support a recently proposed model in which replication origins licensed by excess Mcm2-7 are required for the survival of human cells exposed to replication stress

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

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

<p>Correction: Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches</p

Linage disequilibrium (LD) decay across all linkage groups.

<p>The overall LD decay across the genome is at 5</p