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Conventional breeding approaches have played a significant role in meeting the food demand remarkably well until now. However, the increasing population, yield plateaus in certain crops, and limited recombination necessitate using genomic resources for genomics-assisted crop improvement programs. As a result of advancements in the next-generation sequence technology, GABs have developed dramatically to characterize allelic variants and facilitate their rapid and efficient incorporation in crop improvement programs. Genomics-assisted breeding (GAB) has played an important role in harnessing the potential of modern genomic tools, exploiting allelic variation from genetic resources and developing cultivars over the past decade. The availability of pangenomes for major crops has been a significant development, albeit with varying degrees of completeness. Even though adopting these technologies is essentially determined on economic grounds and cost-effective assays, which create a wealth of information that can be successfully used to exploit the latent potential of crops. GAB has been instrumental in harnessing the potential of modern genomic resources and exploiting allelic variation for genetic enhancement and cultivar development. GAB strategies will be indispensable for designing future crops and are expected to play a crucial role in breeding climate-smart crop cultivars with higher nutritional value., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: I am working as associate editor in the Journal., (© 2024 The Authors.)

Pigeonpea [ Cajanus cajan (L.) Millspaugh] is a widely grown pulse with high seed protein content that contributes to food and nutritional security in the Indian subcontinent. The majority of pigeonpea varieties cultivated in India are of medium duration (<180 days to maturity), which makes it essential for breeders to focus on the development of stable high-yielding varieties. The diverse agroecological regime in the Indian subcontinent necessitates an efficient multi-environment study by taking into consideration genotype (G) × environment (E) interaction (GEI) that has a significant impact on traits like grain yield (GY) in developing high-yielding and widely adaptable varieties. In the present study, 37 pigeonpea genotypes were evaluated during the 2021 rainy season at ARS Badnapur, ARS Tandur, BAU Ranchi, GKVK Bengaluru, and ICRISAT Patancheru. The GEI was significant on the grain yield ( p < 0.01), and hence, genotype + genotype × environment (GGE) and additive main effects and multiplicative interaction (AMMI) biplots along with AMMI stability value (ASV) and yield relative to environmental maximum (YREM) statistics were used to identify stable high-yielding genotypes. The interaction principal component analysis 1 and 2 (IPC1 and IPC2) explained 40.6% and 23.3% variations, respectively. Based on the rankings of genotypes, G37 (ICPL 20205), G35 (ICPL 20203), G8 (ICPL 19404), G17 (ICPL 19415), and G9 (ICPL 19405) were identified as ideal genotypes. Discriminativeness vs. representativeness identified GKVK Bengaluru as an ideal environment for comprehensive evaluation of test genotypes. However, ICPL 19405 was identified as the potentially stable high-yielding genotype for further testing and release across the test environments based on its mean grain yield (1,469.30 kg/ha), least ASV (3.82), and low yield stability index (YSI) of 13., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Bomma, Shruthi, Soregaon, Gaddameedi, Suma, Pranati, Lohithaswa, Patil, Kumar, Sandeep, Vemula and Gangashetty.)

Storage pests, particularly bruchids, are major biotic constraints causing significant storage losses in pulses. Conventional control methods relying on insecticides and fumigants often lead to food contamination due to toxic pesticide residues and a rapid decline in seed germination. In this investigation, through green nano-technological application, a promising and sustainable alternative for pest management is developed. Silver and copper nanoparticles were synthesized through ocimum leaf extract. The characterization of silver and copper nanoparticles was carried out by UV-spectroscopy, particle size analyzer, scanning electron microscopy, X-ray diffraction, and Fourier-transform infrared. Both the nanoparticles were spherical and crystalline in nature. Greengram seeds were primed with standardized silver and copper nanoparticles at different concentrations (1000, 1500, and 2000 ppm) and compared with castor-treated, deltamethrin-treated, and untreated control seeds for seed quality, growth, and yield. After one month of storage, all the pulse beetles released in different treatments exhibited 100 % mortality, whereas in control, the insects multiplied. At the end of nine months, the control seeds had shown 72 % damage and 39.67 % germination. In contrast, silver nanoparticles at 1000 ppm showed no seed damage and achieved 81.67 % germination, which was on par with copper nanoparticles at 1000 ppm with 79.33 % germination. Seed priming of silver and copper nanoparticles at 1000 ppm also demonstrated superior performance in all the seed quality and biochemical parameters (alpha amylase and catalase) throughout the storage period. Whereas, in the greenhouse experiment, enhanced growth (35.96 cm, 46.48 cm, and 53.00 cm at 30, 60 DAS, and at harvest, respectively) and yield per plant (3.75 g) were significantly higher in plants that were given foliar application with silver nanoparticles at 1000 ppm. Furthermore, foliar application of these nanoparticles at all concentrations (1000, 1500, and 2000 ppm) did not exhibit any adverse effects on soil microbial organisms, as assessed by dehydrogenase enzyme activity. Hence, this research highlights the potential use of silver and copper nanoparticles at 1000 ppm as effective tools for storage pest management and contributing to improved agricultural productivity and sustainability., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

The development of nutrient-use efficient rice lines is a priority amidst the changing climate and depleting resources viz., water, land, and labor for achieving sustainability in rice cultivation. Along with the traditional transplanted irrigated system of cultivation, the dry direct-seeded aerobic system is gaining ground nationwide. The root-related traits play a crucial role in nutrient acquisition, adaptation and need to be concentrated along with the yield-attributing traits. We phenotyped an association panel of 118 rice lines for seedling vigour index (SVI) traits at 14 and 21 days after sowing (DAS), root-related traits at panicle initiation (PI) stage in polythene bags under controlled aerobic condition, yield and yield-related traits under the irrigated condition at ICAR-IIRR, Hyderabad, Telangana; irrigated and aerobic conditions at ARS, Dhadesugur, Raichur, Karnataka. The panel was genotyped using simple sequence repeats (SSR) markers and genome-wide association studies were conducted for identifying marker-trait associations (MTAs). Significant correlations were recorded for root length, root dry weight with SVI, root volume at the PI stage, number of productive tillers per plant, spikelet fertility, the total number of grains per panicle with grain yield per plant under irrigated conditions, and the total number of grains per panicle with grain yield per plant under aerobic condition. The panel was divided into three sub-groups (K = 3) and correlated with the principal component analysis. The maximum number of MTAs were found on chromosomes 2, 3, and 12 with considerable phenotypic variability. Consistent MTAs were recorded for SVI traits at 14 and 21 DAS (RM25310, RM80, RM22961, RM1385), yield traits under irrigated conditions (RM2584, RM5179, RM410, RM20698, RM14753) across years at ICAR-IIRR, grain yield per plant (RM22961, RM1146) under the aerobic condition, grain yield per plant at irrigated ICAR-IIRR and SVI (RM5501), root traits at PI stage (RM2584, RM80, RM410, RM1146, RM18472). Functionally relevant genes near the MTAs through in-silico expression analysis in root and panicle tissues viz., HBF2 bZIP transcription factor, WD40 repeat-like domain, OsPILS6a auxin efflux carrier, WRKY108, OsSCP42, OsMADS80 , nodulin-like domain-containing protein, amino acid transporter using various rice expression databases were identified. The identified MTAs and rice lines having high SVI traits (Langphou, TI-128, Mouli, TI-124, JBB-631-1), high yield under aerobic (Phouren, NPK-43, JBB-684, Ratnamudi, TI-112), irrigated conditions (KR-209, KR-262, Phouren, Keibi-Phou, TI-17), robust root traits like root length (MoirangPhou-Angouba, Wangoo-Phou, JBB-661, Dissi, NPK-45), root volume (Ratnachudi, KJ-221, Mow, Heimang-Phou, PUP-229) can be further employed in breeding programs for the targeted environments aimed at improving seedling vigour, yield-related traits under irrigated condition, aerobic condition as adaptability to water-saving technology., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Padmashree, Barbadikar, Honnappa, Magar, Balakrishnan, Lokesha, Gireesh, Siddaiah, Madhav, Ramesha, Bharamappanavara, Phule, Senguttuvel, Diwan, Subrahmanyam and Sundaram.)

Artocarpus (Moraceae), known as breadfruits for their diverse nutritious fruits, is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a larger tree, Artocarpus hirsutus , also called "Wild Jack" or "Ayani", is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from the sacred groves of Coorg, India. To decipher demographic and evolutionary history, we compared our Wild Jack genome with previously published Jackfruit and Breadfruit genomes. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus . Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus , which had a major contribution to its larger genome size. Several genes from starch, sucrose metabolism, and plant hormone signal transduction pathways, in Artocarpus species had signatures of selection and gene family evolution. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild Jack., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Patil, Vajja, Raghavendra, Satish, Kushalappa and Vijay.)

Fostering a culture of continuous improvement through regular monitoring of genetic trends in breeding pipelines is essential to improve efficiency and increase accountability. This is the first global study to estimate genetic trends across the International Maize and Wheat Improvement Center (CIMMYT) tropical maize breeding pipelines in eastern and southern Africa (ESA), South Asia, and Latin America over the past decade. Data from a total of 4152 advanced breeding trials and 34,813 entries, conducted at 1331 locations in 28 countries globally, were used for this study. Genetic trends for grain yield reached up to 138 kg ha -1  yr -1 in ESA, 118 kg ha -1  yr -1 South Asia and 143 kg ha -1  yr -1 in Latin America. Genetic trend was, in part, related to the extent of deployment of new breeding tools in each pipeline, strength of an extensive phenotyping network, and funding stability. Over the past decade, CIMMYT's breeding pipelines have significantly evolved, incorporating new tools/technologies to increase selection accuracy and intensity, while reducing cycle time. The first pipeline, Eastern Africa Product Profile 1a (EA-PP1a), to implement marker-assisted forward-breeding for resistance to key diseases, coupled with rapid-cycle genomic selection for drought, recorded a genetic trend of 2.46% per year highlighting the potential for deploying new tools/technologies to increase genetic gain., (© 2022. The Author(s).)

Crop yield varies considerably within agroecology depending on the genetic potential of crop cultivars and various edaphic and climatic variables. Understanding site-specific changes in crop yield and genotype × environment interaction are crucial and needs exceptional consideration in strategic breeding programs. Further, genotypic response to diverse agro-ecologies offers identification of strategic locations for evaluating traits of interest to strengthen and accelerate the national variety release program. In this study, multi-location field trial data have been used to investigate the impact of environmental conditions on crop phenological dynamics and their influence on the yield of mungbean in different agroecological regions of the Indian subcontinent. The present attempt is also intended to identify the strategic location(s) favoring higher yield and distinctiveness within mungbean genotypes. In the field trial, a total of 34 different mungbean genotypes were grown in 39 locations covering the north hill zone ( n = 4), northeastern plain zone ( n = 6), northwestern plain zone ( n = 7), central zone ( n = 11) and south zone ( n = 11). The results revealed that the effect of the environment was prominent on both the phenological dynamics and productivity of the mungbean. Noticeable variations (expressed as coefficient of variation) were observed for the parameters of days to 50% flowering (13%), days to maturity (12%), reproductive period (21%), grain yield (33%), and 1000-grain weight (14%) across the environments. The genotype, environment, and genotype × environment accounted for 3.0, 54.2, and 29.7% of the total variation in mungbean yield, respectively ( p < 0.001), suggesting an oversized significance of site-specific responses of the genotypes. Results demonstrated that a lower ambient temperature extended both flowering time and the crop period. Linear mixed model results revealed that the changes in phenological events (days to 50 % flowering, days to maturity, and reproductive period) with response to contrasting environments had no direct influence on crop yields ( p > 0.05) for all the genotypes except PM 14-11. Results revealed that the south zone environment initiated early flowering and an extended reproductive period, thus sustaining yield with good seed size. While in low rainfall areas viz ., Sriganganagar, New Delhi, Durgapura, and Sagar, the yield was comparatively low irrespective of genotypes. Correlation results and PCA indicated that rainfall during the crop season and relative humidity significantly and positively influenced grain yield. Hence, the present study suggests that the yield potential of mungbean is independent of crop phenological dynamics; rather, climatic variables like rainfall and relative humidity have considerable influence on yield. Further, HA-GGE biplot analysis identified Sagar, New Delhi, Sriganganagar, Durgapura, Warangal, Srinagar, Kanpur, and Mohanpur as the ideal testing environments, which demonstrated high efficiency in the selection of new genotypes with wider adaptability., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Parihar, Gupta, Hazra, Lamichaney, Sen Gupta, Singh, Kumar, Singh, Vaishnavi, Jaberson, Das, Dev, Yadav, Jamwal, Choudhary, Khedar, Prakash, Dikshit, Panwar, Katiyar, Kumar, Mahto, Borah, Singh, Das, Patil, Nanda, Kumar, Rajput, Chauhan, Patel, Kanwar, Kumar, Mishra, Kumar, Swarup, Mogali, Kumaresan, Manivannan, Gowda, Pandiyan, Rao, Shivani, Prusti, Mahadevu, Iyanar and Das.)

Development process of rice analogues by utilising the broken rice (BRF) and broken pigeonpea dhal (BPDF) flours together with water and sodium alginate as binding agent through extrusion was carried out. Two variable viz . , BPDF (20, 30 and 40%) and moisture content (25, 30 and 35%) were controlled in the study to produce rice analogue resembling the raw rice. The optimum combination of flour mixture established for 30% BPDF and 30% water content with highest desirability of 0.855. The optimum combination had highest crude protein, carbohydrate and ash contents of 12.70, 71.72 and 0.99%, respectively. The colour values L*, a* and b* were found to be 68.30, 4.62 and 25.91, respectively. The pasting temperature and peak viscosity were 78.68 °C and 23,173.3 cP. The physico-chemical and pasting properties can be modified by altering the different constituents for specific quality requirements., Competing Interests: Conflicts of interestThe authors declare that they have no competing interests., (© Association of Food Scientists & Technologists (India) 2022.)

The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea ( Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers' fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016-2017 and 2018-2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017-2018, 2018-2019, and 2019-2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers.

Pearl millet [ Pennisetum glaucum (L.) R. Br.] is grown under both arid and semi-arid conditions in India, where other cereals are hard to grow. Pearl millet cultivars, hybrids, and OPVs (open pollinated varieties) are tested and released by the All India Coordinated Research Project on Pearl Millet (AICRP-PM) across three zones (A 1 , A, and B) that are classified based on rainfall pattern. Except in locations with extreme weather conditions, hybrids dominate pearl millet growing areas, which can be attributed to hybrid vigor and the active role of the private sector. The importance of OPVs cannot be ruled out, owing to wider adaptation, lower input cost, and timely seed availability to subsidiary farmers cultivating this crop. This study was conducted to scrutinize the presently used test locations for evaluation of pearl millet OPVs across India, identify the best OPVs across locations, and determine the variation in grain Fe and Zn contents across locations in these regions. Six varieties were evaluated across 20 locations in A 1 and A (pooled as A) and B zones along with three common checks and additional three zonal adapted checks in the respective zones during the 2019 rainy season. Recorded data on yield and quality traits were analyzed using genotype main effects and genotype × environment interaction biplot method. The genotype × environment (G × E) interaction was found to be highly significant for all the grain yield and agronomic traits and for both micronutrients (iron and zinc). However, genotypic effect (G) was four (productive tillers) to 49 (grain Fe content) times that of G × E interaction effect for various traits across zones that show the flexibility of OPVs. Ananthapuramu is the ideal test site for selecting pearl millet cultivars effectively for adaptation across India, while Ananthapuramu, Perumallapalle, and Gurugram can also be used as initial testing locations. OPVs MP 599 and MP 600 are identified as ideal genotypes, because they showed higher grain and fodder yields and stability compared with other cultivars. Iron and zinc concentration showed highly significant positive correlation (across environment = 0.83; p < 0.01), indicating possibility of simultaneous effective selection for both traits. Three common checks were found to be significantly low yielders than the test entries or zonal checks in individual zones and across India, indicating the potential of genetic improvement through OPVs., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Sanjana Reddy, Satyavathi, Khandelwal, Patil, Gupta, Sharma, Mungra, Singh, Narasimhulu, Bhadarge, Iyanar, Tripathi, Yadav, Bhardwaj, Talwar, Tiwari, Kachole, Sravanti, Shanthi Priya, Athoni, Anuradha, Govindaraj, Nepolean and Tonapi.)

The complexity of genotype × environment interactions under drought reduces heritability, which determines the effectiveness of selection for drought tolerance and development of drought tolerant varieties. Genetic progress measured through changes in yield performance over time is important in determining the efficiency of breeding programmes in which test cultivars are replaced each year on the assumption that the new cultivars will surpass the older cultivars. The goal of our study was to determine the annual rate of genetic gain for rice grain yield in a drought-prone rainfed system in a series of multi-environment trials conducted from 2005 to 2014 under the Drought Breeding Network of Indian sites in collaboration with the International Rice Research Institute (IRRI). Our results show a positive trend in grain yield with an annual genetic yield increase of about 0.68 % under irrigated control, 0.87 % under moderate reproductive stage drought stress and 1.9 % under severe reproductive stage drought stress due to breeding efforts. The study also demonstrates the effectiveness of direct selection for grain yield under both irrigated control as well as managed drought stress screening to improve yield in typical rainfed systems. IRRI's drought breeding programme has exhibited a significant positive trend in genetic gain for grain yield over the years under both drought stress as well as favorable irrigated control conditions. Several drought tolerant varieties released from the programme have outperformed the currently grown varieties under varied conditions in the rainfed environments on farmers' fields., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Authors.)

Spatio-temporal and developmental stage-specific transcriptome analysis plays a crucial role in systems biology-based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world's widest cultivated subsp. fastigiata based on RNA-seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired-end filtered reads were generated followed by identification of 81 901 transcripts from an early-maturing, high-yielding, drought-tolerant groundnut variety, ICGV 91114. Further, 57 344 genome-wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in-depth analysis of the global transcriptome sheds light into complex regulatory networks namely gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer-friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits., (© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Key Message: Comparative assessment identified naïve interaction model, and naïve and informed interaction GS models suitable for achieving higher prediction accuracy in groundnut keeping in mind the high genotype × environment interaction for complex traits. Genomic selection (GS) can be an efficient and cost-effective breeding approach which captures both small- and large-effect genetic factors and therefore promises to achieve higher genetic gains for complex traits such as yield and oil content in groundnut. A training population was constituted with 340 elite lines followed by genotyping with 58 K 'Axiom&#95;Arachis' SNP array and phenotyping for key agronomic traits at three locations in India. Four GS models were tested using three different random cross-validation schemes (CV0, CV1 and CV2). These models are: (1) model 1 (M1 = E + L) which includes the main effects of environment (E) and line (L); (2) model 2 (M2 = E + L + G) which includes the main effects of markers (G) in addition to E and L; (3) model 3 (M3 = E + L + G + GE), a naïve interaction model; and (4) model 4 (E + L + G + LE + GE), a naïve and informed interaction model. Prediction accuracy estimated for four models indicated clear advantage of the inclusion of marker information which was reflected in better prediction accuracy achieved with models M2, M3 and M4 as compared to M1 model. High prediction accuracies (> 0.600) were observed for days to 50% flowering, days to maturity, hundred seed weight, oleic acid, rust@90 days, rust@105 days and late leaf spot@90 days, while medium prediction accuracies (0.400-0.600) were obtained for pods/plant, shelling  %, and total yield/plant. Assessment of comparative prediction accuracy for different GS models to perform selection for untested genotypes, and unobserved and unevaluated environments provided greater insights on potential application of GS breeding in groundnut.

Key Message: Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era.

Annigeri 1 and JG 74 are elite high yielding desi cultivars of chickpea with medium maturity duration and extensively cultivated in Karnataka and Madhya Pradesh, respectively. Both cultivars, in recent years, have become susceptible to race 4 of Fusarium wilt (FW). To improve Annigeri 1 and JG 74, we introgressed a genomic region conferring resistance against FW race 4 ( foc4 ) through marker-assisted backcrossing using WR 315 as the donor parent. For foreground selection, TA59, TA96, TR19 and TA27 markers were used at Agricultural Research Station, Kalaburagi, while GA16 and TA96 markers were used at Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur. Background selection using simple sequence repreats (SSRs) for the cross Annigeri 1 × WR 315 in BC 1 F 1 and BC 2 F 1 lines resulted in 76-87% and 90-95% recurrent parent genome recovery, respectively. On the other hand, 90-97% genome was recovered in BC 3 F 1 lines in the case of cross JG 74 × WR 315. Multilocation evaluation of 10 BC 2 F 5 lines derived from Annigeri 1 provided one superior line referred to as Super Annigeri 1 with 8% increase in yield and enhanced disease resistance over Annigeri 1. JG 74315-14, the superior line in JG 74 background, had a yield advantage of 53.5% and 25.6% over the location trial means in Pantnagar and Durgapura locations, respectively, under Initial Varietal Trial of All India Coordinated Research Project on Chickpea. These lines with enhanced resistance and high yield performance are demonstration of successful deployment of molecular breeding to develop superior lines for FW resistance in chickpea., Competing Interests: Compliance with ethical standardsThe authors declare that they have no conflict of interest.

G-box-binding factors are plant transcription factors, involved in a wide range of biological processes including abiotic stress responses. In this study, we analyzed the expression of OsGBF1 during salt stress in two contrasting Oryza sativa spp. indica genotypes, Rasi and Tellahamsa . Two-day-old seedlings were exposed to NaCl stress under two different conditions. One set was exposed to 100 mM NaCl before transferring to 250 mM (induction stress), while another set was transferred directly to 250 mM (shock stress). During early induction stress, OsGBF1 was up-regulated in Rasi when compared to Tellahamsa . We cloned full-length OsGBF1 from these two genotypes, and analyzed the sequences. Our analysis indicated the presence of transcript variants, which are designated as OsGBF1a and 1b. OsGBF1b variant retained introns, which lead to the generation of premature termination codon. OsGBF1b transcript levels were not significantly different at 12-h of induction stress in Tellahamsa and Rasi . At 24-h of shock stress, OsGBF1b was up-regulated in both genotypes and the transcript was more in Rasi . Since, OsGBF1a and 1b are predicted to be splice variants, we examined expression pattern of OsSKIP , a splicing factor and component of the spliceosome. In induction stress, OsSKIP was up-regulated at 12- and 24-h in Rasi when compared to Tellahamsa . On the contrary, at 24-h shock stress, OsSKIP was down-regulated in Rasi when compared to Tellahamsa . It is possible that OsSKIP expression was increased in Rasi during induction stress for accurate splicing that could aid in tolerance. This is the first report on OsGBF1 splice variant and the variant could have specific functions linked to stress tolerance in rice., Competing Interests: Compliance with ethical standardsThe authors declare that they have no conflict of interest.The research has been conducted with the consent of the authorities and that the research does not involve human participants and/or animals.

Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion-deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species., (© 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding. Using genome-wide association analysis, we identify associations between several candidate genes and agronomically important traits. Candidate genes for these traits in pigeonpea have sequence similarity to genes functionally characterized in other plants for flowering time control, seed development and pod dehiscence. Our findings will allow acceleration of genetic gains for key traits to improve yield and sustainability in pigeonpea.

Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL&#95;A and ICPL 20096 × ICPL 332 designated as PRIL&#95;B) and one F 2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL&#95;A, PRIL&#95;B and F 2 , respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.

To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing-based bulked segregant analysis (Seq-BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP index was calculated between R- and S-bulks with the help of draft genome sequence and reference-guided assembly of ICPL 20096 (resistant parent). Seq-BSA has provided seven candidate SNPs for FW and SMD resistance in pigeonpea. In parallel, four additional genotypes were re-sequenced and their combined analysis with R- and S-bulks has provided a total of 8362 nonsynonymous (ns) SNPs. Of 8362 nsSNPs, 60 were found within the 2-Mb flanking regions of seven candidate SNPs identified through Seq-BSA. Haplotype analysis narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by re-sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis revealed association of four candidate nsSNPs in four genes with FW resistance and four candidate nsSNPs in three genes with SMD resistance. Further, In silico protein analysis and expression profiling identified two most promising candidate genes namely C.cajan&#95;01839 for SMD resistance and C.cajan&#95;03203 for FW resistance. Identified candidate genomic regions/SNPs will be useful for genomics-assisted breeding in pigeonpea., (© 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

An investigation on inheritance of qualitative traits in dolichos bean revealed biallelic monogenic control of photoperiodinduced sensitivity to flowering time and flower colour in F₂ and F₂ generations. While, growth habit and pod curvature are each controlled by two genes that exhibit classical complementary epistasis, raceme emergence was controlled by two genes that displayed classical inhibitory epistasis. The dominant alleles, at two different unlinked pairs of genes are necessary for plants to exhibit indeterminate growth habit and bear straight pods. Any other combination of alleles at the two pairs of genes result in plants displaying determinate growth habit and bearing curved pods.While, the genes controlling growth habit, PSFT and raceme emergence are linked. Those controlling flower colour and pod curvature are segregated independent of each other. These results are discussed in relation to strategies for breeding dolichos bean.

Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the 'reference set' of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15-20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (p value > 2.1 × 10-6) with wide phenotypic variance (PV) range (5.81-90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.

Studies were undertaken to identify pigeonpea, Cajanus cajan (L.) Millspaugh and the wild relative of pigeonpea, Cajanus scarabaeoides (L.) (accession ICPW 125,) genotypes that are hospitable to the pod borer, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) larval parasitoid, Campoletis chlorideae Uchida (Hymenoptera: Ichneumonidae) for the management of this pest in pigeonpea based cropping systems. Percentage parasitization of the H. armigera larvae by the C. chlorideae females was greater under no-choice conditions than under multi-choice conditions because of forced parasitization under no-choice conditions. Lowest parasitization was recorded on the wild relative, ICPW 125, which may be due to long nonglandular hairs and low survival of H. armigera larvae. Parasitization of H. armigera larvae was greater under no-choice, dual-choice and/or multi-choice conditions on ICPL 87, ICPL 87119 and ICPL 87091, which are susceptible to H. armigera, than on the pod borer-resistant genotypes ICPL 332WR, ICPL 84060 and ICPB 2042; while survival and development of the parasitoid was better on H. armigera larvae fed on ICPL 87, ICPL 87119, LRG 41, ICP 7035 and ICPL 87091 than on ICPL 332WR, ICPL 84060, ICPB 2042 and ICPW 125. The genotypes ICPL 87, ICPL 87119, LRG 42 and ICPL 87091 that are hospitable to C. chloridae, are better suited for use in integrated pest management to minimize the losses due to H. armigera in pigeonpea.

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 x 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 (QTL(rust)01), 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 x 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.