Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties.

Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties.

High confidence QTLs and key genes identified using Meta-QTL analysis for enhancing heat tolerance in chickpea (Cicer arietinum L.).

The rising global temperatures seriously threaten sustainable crop production, particularly the productivity and production of heat-sensitive crops like chickpeas. Multiple QTLs have been identified to enhance the heat stress tolerance in chickpeas, but their successful use in breeding programs remains limited. Towards this direction, we constructed a high-density genetic map spanning 2233.5 cM with 1069 markers. Using 138 QTLs reported earlier, we identified six Meta-QTL regions for heat tolerance whose confidence interval was reduced by 2.7-folds compared to the reported QTLs. Meta-QTLs identified on CaLG01 and CaLG06 harbor QTLs for important traits, including days to 50% flowering, days to maturity, days to flower initiation, days to pod initiation, number of filled pods, visual score, seed yield per plant, biological yield per plant, chlorophyll content, and harvest index. In addition, key genes identified in Meta-QTL regions like Pollen receptor-like kinase 3 (CaPRK3), Flowering-promoting factor 1 (CaFPF1), Flowering Locus C (CaFLC), Heat stress transcription factor A-5 (CaHsfsA5), and Pollen-specific leucine-rich repeat extensins (CaLRXs) play an important role in regulating the flowering time, pollen germination, and growth. The consensus genomic regions, and the key genes reported in this study can be used in genomics-assisted breeding for enhancing heat tolerance and developing heat-resilient chickpea cultivars.

Optimizing hybrid vigor: a comprehensive analysis of genetic distance and heterosis in eggplant landraces.

Introduction: This study explored the molecular characterization of 14 eggplant (brinjal) genotypes to evaluate their genetic diversity and the impact of heterosis. As eggplant is a vital horticultural crop with substantial economic and nutritional value, a comprehensive understanding of its genetic makeup and heterosis effects is essential for effective breeding strategies. Our aim was not only to dissect the genetic diversity among these genotypes but also to determine how genetic distance impacts heterotic patterns, which could ultimately help improve hybrid breeding programs. Methods: Genetic diversity was assessed using 20 SSR markers, and the parental lines were grouped into five clusters based on the Unweighted Pair Group Method of Arithmetic Means (UPGMA). Heterosis was examined through yield and yield-related traits among parents and hybrids. Results: Polymorphisms were detected in eight out of the twenty SSR markers across the parental lines. Notably, a high genetic distance was observed between some parents. The analysis of yield and yield-related traits demonstrated significant heterosis over mid, superior, and standard parents, particularly in fruit yield per plant. Two crosses (RKML-26 X PPC and RKML1 X PPC) displayed substantial heterosis over mid and better parents, respectively. However, the positive correlation between genetic distance and heterosis was only up to a certain threshold; moderate genetic distance often resulted in higher heterosis compared to very high genetic distance. Discussion: These findings emphasize the critical role of parental selection in hybrid breeding programs. The results contribute to the understanding of the relationship between genetic distance and heterosis, and it is suggested that future research should delve into the genetic mechanisms that drive heterosis and the effect of genetic distance variance on heterosis. The insights drawn from this study can be harnessed to enhance crop yield and economic value in breeding programs.

Assessing the heat sensitivity of Urdbean (Vigna mungo L. Hepper) genotypes involving physiological, reproductive and yield traits under field and controlled environment.

The rising temperatures are seriously impacting the food crops, including urdbean; hence efforts are needed to identify the sources of heat tolerance in such crops to ensure global food security. In the present study, urdbean genotypes were evaluated for heat tolerance under natural outdoor for two consecutive years (2018, 2019) and subsequently in the controlled environment of the growth chamber to identify high temperature tolerant lines. The genotypes were assessed involving few physiological traits (membrane damage, chlorophyll, photosynthetic efficiency, stomatal conductance, lipid peroxidation), reproductive traits (pollen germination % and pollen viability %) and yield related traits (total number of pods plant-1, total seeds plant-1, single seed weight and seed yield plant-1). Based upon these tested traits, PantU31, Mash114, UTTARA and IPU18-04 genotypes were identified as promising genotypes for both years under heat stress condition. Further confirming heat tolerance, all these four tolerant and four sensitive genotypes were tested under controlled environment under growth chamber condition. All these four genotypes PantU31, Mash114, UTTARA and IPU18-04 showed high chlorophyll content, photosynthetic efficiency, stomatal conductance, leaf area, pods plant-1, total seeds plant-1 and low reduction in pollen germination % and pollen viability under stress heat stress condition. Moreover, yield and yield related traits viz., pods plant-1, seeds plant-1, single seed weight and seed yield plant-1 showed very strong positive correlation with pollen germination and pollen viability except electrolyte leakage and malondialdehyde content. Thus, these genotypes could be potentially used as donors for transferring heat tolerance trait to the elite yet heat-sensitive urdbean cultivars.

Response of Physiological, Reproductive Function and Yield Traits in Cultivated Chickpea (Cicer arietinum L.) Under Heat Stress.

Under global climate change, high-temperature stress is becoming a major threat to crop yields, adversely affecting plant growth, and ultimately resulting in significant yield losses in various crops, including chickpea. Thus, identifying crop genotypes with increased heat stress (HS) tolerance is becoming a priority for chickpea research. Here, we assessed the response of seven physiological traits and four yield and yield-related traits in 39 chickpea genotypes grown in normal-sown and late-sown environments [to expose plants to HS (>32/20°C) at the reproductive stage] for two consecutive years (2017-2018 and 2018-2019). Significant genetic variability for the tested traits occurred under normal and HS conditions in both years. Based on the tested physiological parameters and yield-related traits, GNG2171, GNG1969, GNG1488, PantG186, CSJ515, RSG888, RSG945, RVG202, and GNG469 were identified as promising genotypes under HS. Further, ten heat-tolerant and ten heat-sensitive lines from the set of 39 genotypes were validated for their heat tolerance (32/20°C from flowering to maturity) in a controlled environment of a growth chamber. Of the ten heat-tolerant genotypes, GNG1969, GNG1488, PantG186, RSG888, CSJ315, and GNG1499 exhibited high heat tolerance evidenced by small reductions in pollen viability, pollen germination, and pod set %, high seed yield plant-1 and less damage to membranes, photosynthetic ability, leaf water status, and oxidative processes. In growth chamber, chlorophyll, photosynthetic efficiency, pollen germination, and pollen viability correlated strongly with yield traits. Thus, GNG1969, GNG1488, PantG186, RSG888, CSJ315, and GNG1499 genotypes could be used as candidate donors for transferring heat tolerance traits to high-yielding heat-sensitive varieties to develop heat-resilient chickpea cultivars.

Capturing Genetic Variability and Identification of Promising Drought-Tolerant Lines in Exotic Landrace Derived Population Under Reproductive Drought Stress in Rice.

Drought is one of the most predominant abiotic stresses in this century, leading to a drastic reduction in the yield of rainfed rice ecosystems. Breeding of drought-resilient rice varieties is very much in demand for sustainable rice production in drought-prone rainfed ecology. An experiment was designed under irrigated non-stress and drought-stress situations involving an exotic drought-tolerant landrace (Chao Khaw) and a high-yielding aromatic rice cultivar (Kasturi), and an F2:4 derived population of 156 breeding lines was developed at IRRI South Asia Hub, Hyderabad. The objective of the study was to assess the genetic variability, drought tolerance behavior, and identify promising breeding lines for different rice ecologies and drought breeding programs. Restricted maximum likelihood (REML) analysis using the mixed model approach revealed a considerable genetic variation in the population for yield and yield contributing traits in non-stress and drought-stress conditions. We observed very high heritability for all the selected traits under stress 2015 WS (73.8% to 85.3%) and 2016 WS (72.4% to 93.5%) and non-stress 2015 WS (68.2% To 92.9%) and 2016 WS (61.4% to 92.6%) environments, indicating possible selection for grain yield under drought stress and non-stress with the same precision level. None of the secondary traits except harvest index and biomass included in our study showed a positive association with grain yield, indicating indirect selection's ineffectiveness in improving yield under drought. A total of 48 promising breeding lines were found to have a better yield than donor Chao Khaw (up to 38% advantage) and popular drought-tolerant cultivars Shabhagidhan (up to 48% advantage) in stress conditions and recommended for rainfed upland ecology, 34 breeding lines under the well-watered condition suited for rainfed lowland ecology. Overall, the study found 21 common breeding lines that showed their superiority in non-stress and under drought stress situations, fitting best in rainfed lowland ecology with occasional drought occurrence. The large genetic variation found in this population can be exploited further to develop a few forward breeding high-yielding lines with better drought tolerance ability and used as drought donors in drought breeding programs.

Utilizing Wild Cajanus platycarpus, a Tertiary Genepool Species for Enriching Variability in the Primary Genepool for Pigeonpea Improvement.

The use of crop wild relatives in the breeding program has been well recognized to diversify the genetic base along with introgression of useful traits. Cajanus platycarpus (Benth.) Maesen, an annual wild relative belonging to the tertiary genepool of pigeonpea, possesses many useful traits such as early maturity, high protein content, photoperiod insensitivity, and pod borer tolerance for the genetic improvement of cultivated pigeonpea. Using this cross incompatible wild Cajanus species, an advanced backcross population was developed following the embryo rescue technique. In the present study, a pre-breeding population consisting of 136 introgression lines (ILs) along with five popular varieties (used as checks) was evaluated for important agronomic traits during 2016 and 2017 rainy seasons and for grain nutrient content during 2016, 2017, and 2018 rainy seasons. Large genetic variation was observed for agronomic traits such as days to 50% flowering, number of pods per plant, pod weight per plant, grain yield per plant, and grain nutrients [protein content, grain iron (Fe), zinc (Zn), calcium (Ca), and magnesium (Mg)] in the pre-breeding population. Significant genotype × environment interaction was also observed for agronomic traits as well as grain nutrients indicating the sensitivity of these traits to the environments. No significant correlations were observed between grain yield and grain nutrients except grain Zn content which was negatively correlated with grain yield. Overall, 28 promising high-yielding ILs with high grain nutrient content were identified. These ILs, in particular, ICPP # 171012, 171004, 171102, 171087, 171006, and 171050 flowered significantly earlier than the popular mega variety, ICPL 87119 (Asha) and thus hold potential in developing new short-duration cultivars. The comprehensive multi-site assessment of these high-yielding, nutrient-rich accessions would be useful in identifying region-specific promising lines for direct release as cultivars. Moreover, these ILs are expected to replace the popular existing cultivars or for use as new and diverse sources of variations in hybridization programs for pigeonpea improvement.

Evaluation and Identification of Promising Introgression Lines Derived From Wild Cajanus Species for Broadening the Genetic Base of Cultivated Pigeonpea [Cajanus cajan (L.) Millsp.].

Pigeonpea [Cajanus cajan (L.) Millsp.], a multipurpose and nutritious grain legume crop, is cultivated for its protein-rich seeds mainly in South Asia and Eastern and Southern Africa. In spite of large breeding efforts for pigeonpea improvement in India and elsewhere, genetic enhancement is inadequate largely due to its narrow genetic base and crop susceptibility to stresses. Wild Cajanus species are novel source of genetic variations for the genetic upgradation of pigeonpea cultivars. In the present study, 75 introgression lines (ILs), derived from crosses involving cultivated pigeonpea variety ICPL 87119 and wild Cajanus cajanifolius and Cajanus acutifolius from the secondary gene pool, were evaluated for yield and yield-attributing traits in diverse environments across locations and years. Restricted maximum likelihood (REML) analysis revealed large genetic variations for days to 50% flower, days to maturity, plant height, primary branches per plant, pods per plant, pod weight per plant, 100-seed weight, and grain yield per plant. Superior ILs with mid-early to medium maturity duration identified in this study are useful genetic resources for use in pigeonpea breeding. Additive main effects and multiplicative interaction (AMMI) analysis unfolded large influence of environment and genotype × environment interaction for variations in yield. A few lines such as ICPL 15023 and ICPL 15072 with yield stability were identified, while a number of lines were completely resistant (0%) to sterility mosaic diseases and/or Fusarium wilt. These lines are novel genetic resources for broadening the genetic base of pigeonpea and bring yield stability and stress tolerance. High-yielding lines ICPL 15010, ICPL 15062, and ICPL 15072 have been included in the initial varietal trials (IVTs) of the All India Coordinated Research Project (AICRP) on pigeonpea for wider evaluation across different agro-ecological zones in India for possible release as variety(ies).

Molecular Mapping of QTLs for Heat Tolerance in Chickpea.

Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL × environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea.