Introgression Breeding Research Articles

Utilization of the Dasypyrum genus for genetic improvement of wheat.

The Dasypyrum genus species are found predominantly in the Mediterranean region. They possess an array of agronomically essential traits, such as resistance to biotic and abiotic stresses, high protein content, and better grain quality, and are thus a valuable genetic resources for wheat improvement. In recent decades, there has been significant progress in the development of wheat-Dasypyrum genetic stocks, leading to the successful transfer of beneficial genes from Dasypyrum into cultivated wheat. Notably, the chromosome-scale genome assembly of Dasypyrum villosum was preliminarily completed in 2023, laying the groundwork for functional genomics research and wheat-Dasypyrum introgression breeding. This article aims to provide a concise overview of the relationships between different species belonging to the Dasypyrum genus, the development of wheat-Dasypyrum genetic stocks, the desirable genes derived from Dasypyrum, and the molecular and cytogenetic markers that could be used to identify Dasypyrum chromatins. These insights can assist wheat breeders in utilizing the Dasypyrum genus in future wheat breeding endeavors.

Exploitation of the genetic potential of Thinopyrum and Agropyron genera to protect wheat from diseases and environmental stresses.

Common wheat is one of the most important food crops in the world. Grain harvests can be increased by reducing losses from diseases and environmental stresses. The tertiary gene pool, including Thinopyrum spp., is a valuable resource for increasing genetic diversity and wheat resistance to fungal diseases and abiotic stresses. Distant hybridization between wheat and Thinopyrum spp. began in the 1920s in Russia, and later continued in different countries. The main results were obtained using the species Th. ponticum and Th. intermedium. Additionally, introgression material was created based on Th. elongatum, Th. bessarabicum, Th. junceiforme, Agropyron cristatum. The results of introgression for resistance to diseases (leaf, stem, and stripe rusts; powdery mildew; Fusarium head blight; and Septoria blotch) and abiotic stresses (drought, extreme temperatures, and salinity) to wheat was reviewed. Approaches to improving the agronomic properties of introgression breeding material (the use of irradiation, ph-mutants and compensating Robertsonian translocations) were described. The experience of long-term use in the world of a number of genes from the tertiary gene pool in protecting wheat from leaf and stem rust was observed. Th. ponticum is a nonhost for Puccinia triticina (Ptr) and P. graminis f. sp. tritici (Pgt) and suppresses the development of rust fungi on the plant surface. Wheat samples with the tall wheatgrass genes Lr19, Lr38, Sr24, Sr25 and Sr26 showed defence mechanisms similar to nonhosts resistance. Their influence led to disruption of the development of surface infection structures and fungal death when trying to penetrate the stomata (prehaustorial resistance or stomatal immunity). Obviously, a change in the chemical properties of fungal surface structures of races virulent to Lr19, Lr24, Sr24, Sr25, and Sr26 leads to a decrease in their adaptability to the environment. This possibly determined the durable resistance of cultivars to leaf and stem rusts in different regions. Alien genes with a similar effect are of interest for breeding cultivars with durable resistance to rust diseases and engineering crops with the help of molecular technologies.

A catalogue of recombination coldspots in interspecific tomato hybrids.

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties.

Investigating the genetic control of plant development in spring barley under speed breeding conditions

Key messageThis study found that the genes, PPD-H1 and ELF3, control the acceleration of plant development under speed breeding, with important implications for optimizing the delivery of climate-resilient crops.Speed breeding is a tool to accelerate breeding and research programmes. Despite its success and growing popularity with breeders, the genetic basis of plant development under speed breeding remains unknown. This study explored the developmental advancements of barley genotypes under different photoperiod regimes. A subset of the HEB-25 Nested Association Mapping population was evaluated for days to heading and maturity under two contrasting photoperiod conditions: (1) Speed breeding (SB) consisting of 22 h of light and 2 h of darkness, and (2) normal breeding (NB) consisting of 16 h of light and 8 h of darkness. GWAS revealed that developmental responses under both conditions were largely controlled by two loci: PPDH-1 and ELF3. Allelic variants at these genes determine whether plants display early flowering and maturity under both conditions. At key QTL regions, domesticated alleles were associated with late flowering and maturity in NB and early flowering and maturity in SB, whereas wild alleles were associated with early flowering under both conditions. We hypothesize that this is related to the dark-dependent repression of PPD-H1 by ELF3 which might be more prominent in NB conditions. Furthermore, by comparing development under two photoperiod regimes, we derived an estimate of plasticity for the two traits. Interestingly, plasticity in development was largely attributed to allelic variation at ELF3. Our results have important implications for our understanding and optimization of speed breeding protocols particularly for introgression breeding and the design of breeding programmes to support the delivery of climate-resilient crops.

Characterisation and mapping of a Globodera pallida resistance derived from the wild potato species Solanum spegazzinii

Key messageA new resistance locus acting against the potato cyst nematode Globodera pallida was mapped to chromosome VI in the diploid wild potato species Solanum spegazzinii CPC 7195.The potato cyst nematodes (PCN) Globodera pallida and Globodera rostochiensis are economically important potato pests in almost all regions where potato is grown. One important management strategy involves deployment through introgression breeding into modern cultivars of new sources of naturally occurring resistance from wild potato species. We describe a new source of resistance to G. pallida from wild potato germplasm. The diploid species Solanum spegazzinii Bitter accession CPC 7195 shows resistance to G. pallida pathotypes Pa1 and Pa2/3. A cross and first backcross of S. spegazzinii with Solanum tuberosum Group Phureja cultivar Mayan Gold were performed, and the level of resistance to G. pallida Pa2/3 was determined in progeny clones. Bulk-segregant analysis (BSA) using generic mapping enrichment sequencing (GenSeq) and genotyping-by-sequencing were performed to identify single-nucleotide polymorphisms (SNPs) that are genetically linked to the resistance, using S. tuberosum Group Phureja clone DM1-3 516 R44 as a reference genome. These SNPs were converted into allele-specific PCR assays, and the resistance was mapped to an interval of roughly 118 kb on chromosome VI. This newly identified resistance, which we call Gpa VIlspg, can be used in future efforts to produce modern cultivars with enhanced and broad-spectrum resistances to the major pests and pathogens of potato.

Genetic diversity, disease resistance, and environmental adaptation of Arachis duranensis L.: New insights from landscape genomics.

The genetic diversity that exists in natural populations of Arachis duranensis, the wild diploid donor of the A subgenome of cultivated tetraploid peanut, has the potential to improve crop adaptability, resilience to major pests and diseases, and drought tolerance. Despite its potential value for peanut improvement, limited research has been focused on the association between allelic variation, environmental factors, and response to early (ELS) and late leaf spot (LLS) diseases. The present study implemented a landscape genomics approach to gain a better understanding of the genetic variability of A. duranensis represented in the ex-situ peanut germplasm collection maintained at the U.S. Department of Agriculture, which spans the entire geographic range of the species in its center of origin in South America. A set of 2810 single nucleotide polymorphism (SNP) markers allowed a high-resolution genome-wide characterization of natural populations. The analysis of population structure showed a complex pattern of genetic diversity with five putative groups. The incorporation of bioclimatic variables for genotype-environment associations, using the latent factor mixed model (LFMM2) method, provided insights into the genomic signatures of environmental adaptation, and led to the identification of SNP loci whose allele frequencies were correlated with elevation, temperature, and precipitation-related variables (q < 0.05). The LFMM2 analysis for ELS and LLS detected candidate SNPs and genomic regions on chromosomes A02, A03, A04, A06, and A08. These findings highlight the importance of the application of landscape genomics in ex situ collections of peanut and other crop wild relatives to effectively identify favorable alleles and germplasm for incorporation into breeding programs. We report new sources of A. duranensis germplasm harboring adaptive allelic variation, which have the potential to be utilized in introgression breeding for a single or multiple environmental factors, as well as for resistance to leaf spot diseases.

Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies

The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.

Introgressed eggplant lines with the wild Solanum incanum evaluated under drought stress conditions1

As access to irrigation water becomes increasingly limited, introgression of relevant genomic regions from drought-tolerant wild genotypes is a promising breeding strategy for crop plants. In this study, nine eggplant (Solanum melongena) introgression lines (ILs) covering altogether 71.6% of the genome of the donor wild relative parent S. incanum were evaluated for drought tolerance under water stress conditions. Plants at the five true leaves stage were irrigated at either 100% (control) or 30% (water stress) field capacity for 14 days, and growth and biochemical traits were measured. Reduced irrigation resulted in decreased growth and increased levels of stress markers such as proline and malondialdehyde. Most ILs had lower growth and biomass production than the cultivated parent under both conditions. However, the wild alleles for two genomic regions related to stem and root dry weight (dwt8 and dwr6%) conferred improved tolerance to water stress. In addition, several S. incanum alleles had a positive effect on important traits that may improve yield under drought conditions, such as leaf water content (lwc12%), water use efficiency (wue1%) and chlorophyll content (chl2 and chl8%). Fine-mapping of the genomic regions for tolerance and reducing linkage drag with regions affecting growth will be crucial for significantly improving eggplant drought tolerance through introgression breeding.

Introgression breeding in asparagus – from genetic resources to breeding approach

Introgression breeding in asparagus – from genetic resources to breeding approach

Noor-2019: A High Yielding and Wilt Resistant Chickpea Kabuli (Cicer arietinum L.) Variety Developed through Introgression Breeding

Noor-2019: A High Yielding and Wilt Resistant Chickpea Kabuli (Cicer arietinum L.) Variety Developed through Introgression Breeding

Exploring genetic diversity of potential legume, Vigna angularis (Willd.) Ohwi and Ohashi through agro-morphological traits and SSR markers analysis.

Adzuki bean, an underutilized grain legume, has a significant potential for enhancing food and nutritional security. The main obstacles to developing new cultivars and promoting the adzuki bean as a mainstream pulse crop are a lack of awareness about its potential and insufficient information on crop its genetic diversity. Here, we aimed to explore the untapped potential of adzuki bean germplasm by evaluating its agro-morphological traits and diversity at the molecular level and also to identify trait-specific germplasm by utilizing 100 adzuki bean accessions conserved in the Indian National Genebank. Significant variations was recorded for the morphological traits and identified promising accessions exhibiting desirable traits, such as early flowering (IC341945, EC340257 and EC340283), number of primary branches (IC341945 and IC469175), number of clusters per plant (EC000264, IC167611 and IC341939), number of pods per plant (IC469175, EC34264, EC000264), early maturity (EC340283; EC120460; IC341941) and number of seeds per pod (EC340240, IC455396 and IC341955). Molecular characterization of diverse accessions using 22 polymorphic SSR markers identified a total of 50 alleles, with a mean of 2.27 alleles per loci. The polymorphic information content (PIC) ranged from 0.03 to 0.46, indicating informativeness of markers in distinguishing diverse accessions. Further, the gene diversity among the accessions ranged from 0.03 to 0.57 with a mean of 0.19. Population structure analysis grouped the accessions into three genetic groups, supported by Principal Coordinate Analysis (PCoA) and a phylogenetic tree. Additionally, Analysis of Molecular Variance (AMOVA) confirmed a substantial genetic diversity among the adzuki bean accessions. Thus, the combined assessment of agro-morphological traits and molecular markers effectively distinguished adzuki bean accessions and provided valuable insights in understanding untapped variation at both morphological and molecular levels. The promising accessions identified in the study hold potential for integration into legume improvement programs through introgression breeding, contributing to the development of adzuki bean varieties with target trait.

Study of wild barley species in Southern Dagestan conditions

Wild-growing barley is widely distributed in Dagestan from the coastal lowland to the subalpine zone and is a good fodder and soil-strengthening plant. The study of wild-growing species of barley in the aspect: distribution, systematic diversity, significance are devoted to the works of prominent scientists (Vavilov, Grossheim, Lvov, Kobylyansky, Omarov, Zhukovsky, Tsvelev), which, in the context of the distribution and use of species of the genus Barley in Dagestan, are summarized by Omarov D.S. [6] Wild species are of interest as carriers of valuable breeding traits and can be included in breeding and genetic programs for the possible introgression of valuable genes into the cultivated barley genotype in order to create new promising varieties with a high adaptive potential. At the Dagestan Experimental Station of VIR in 2020-2022 a field study of 114 samples of wild-growing barley species from the VIR collection was carried out to identify the breeding value of these "wild" forms of plants. The sample included representatives of five species: H.spontaneum, H.bulbosum, H.murinum, H.hrasdanicum, and H.glaucum of different ecological and geographical origin. The samples were evaluated for resistance to barley fungal diseases widespread in the region (powdery mildew, dwarf and yellow rust). Interspecific and intraspecific differentiation in terms of resistance to these biotic factors is shown. Resistant forms recommended as sources and susceptible forms as testers are noted.

The root system dominates the growth balance between the aboveground and belowground parts of cotton

Growth balance is very important for plants, which is the coordination of resource acquisition between the aboveground and belowground parts. Extensive research has focused on the aboveground portion, and less attention has been given to the root system. Furthermore, the specific regulatory mechanisms responsible for maintaining the growth balance between aboveground and belowground in crops are still unclear. We examined the root/shoot ratio and leaf area/root length ratio in 19 pima cotton (Gossypium barbadense) and 19 upland cotton (Gossypium hirsutum) accessions, and the effects of root traits on the growth balance were explored. The results indicated that growth balance could affect the biomass accumulation of cotton, and the root system was the core part of controlling growth balance. The difference was that the specific root length played a major role in pima cotton, while the root mass fraction was more important in upland cotton. Despite these differences, both types of cotton achieved similar resource acquisition capability through the synergistic effect of mass fraction and morphological characteristics of leaves and roots. Our study is the first to demonstrate that the root system dominates the growth balance in pima and upland cotton. Selecting accessions with similar phenotypes may represent a promising new direction for increasing the success probability of interspecific hybridization and introgression breeding. These findings expand our understanding of the resource acquisition and utilization of crops and provide a valuable perspective for ecological research and crop breeding.

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding.

Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x = 2n = 18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the 3 Lactuca species as core, accessory, and unique. In addition, we identified 3 interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using 3-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicated the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.

A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus.

SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.

Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species

Rice is a vital staple food crop worldwide, providing nutrition and sustenance to a significant portion of the global population. The genetic diversity of cultivated rice species has been significantly reduced during domestication, resulting in the loss of favorable alleles. To overcome this limitation, wild rice species have been used in introgression breeding programs to introduce beneficial alleles. In this study, we performed syntenic and phylogenetic analyses for 10 Oryza species, comprising both cultivar and wild species. Pairwise syntenic analysis revealed 3885 synteny blocks containing 1,023,342 gene pairs among 10 species. O. nivara contained the most blocks that were syntenous with the other nine species. In total, 425 paralogous and orthologous genes were identified for 30 key genes involved in rice breeding. His1 (43), GS3 (28), and qSW5/GW5 (27) had the most paralogous and orthologous genes. For GS3 and qSW5/GW5, two gene transfer events were detected. These findings have implications for rice breeding strategies, particularly with respect to gene pyramiding and introgression breeding programs. This research will contribute to the development of elite cultivars with improved quality and yield to meet the growing global demand for high-quality rice.

Response to selection through introgression breeding in onion (Allium cepa L.)

Development of suitable varieties of onion with high yieldas well as good shelf life through crossing between longand short-day onion was carried out at the Research Farmof ICAR-Directorate of Onion and Garlic Research,Rajgurunagar, Pune in collaboration with ICAR-CITH,Srinagar. A total of 135 crosses were made between available15 exotic onion varieties and 9 short day lines at ICARCITH,Srinagar. The crosses were evaluated in their F2generation and further selection were continued up to F5generation. The experiment was laid out in randomized blockdesign with three replications during rabi seasons toinvestigate the genetic variability and response to selectionamong all the crosses. Top seven progenies which wereselected on the basis of high yield in F2 generation whichwere also good performers in F3 generation with high yieldand other desirable traits. The selected crosses were foundfree from doubles and bolters in F3 generation. This indicatesthe selection done from F2 to F3 generation is effective fordouble and bolter bulbs which certainly helps to increasethe marketable bulb yield. High degree of variation wasobserved for all the traits studied and the difference betweenphenotypic and genotypic coefficient of variation was foundto be narrow for most of the traits. More than 30% marketableyield enhancement was observed in four progenies viz.,Couger × DOGR-595, Reforma × DOGR-595, Mercedes ×Bhima Super and Collina × DOGR-597 in comparison withbest check Bhima Shakti (41.17 t/ha) in F3 generationwhereas, more than 50 t/ha marketable yield was recorded infour progenies viz., Basic × RGO-53, Couger × DOGR-595,Mercedes × Bhima Super and Reforma × DOGR-595 in F3generation.

Conventional and new genetic resources for an eggplant breeding revolution.

Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. Eggplant is closely related to over 500 species of Solanum subgenus Leptostemonum, belonging to its primary, secondary, and tertiary genepools, and exhibits a wide range of characteristics, including adaptive traits to climate change, that are useful for eggplant breeding. Germplasm banks worldwide hold more than 19,000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in eggplant relatives can greatly contribute to a revolution in eggplant breeding. The recent creation of new genetic resources, such as mutant libraries, core collections, recombinant inbred lines (RILs), and sets of introgression lines (ILs) will be another crucial element for an eggplant breeding revolution, which will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.

Categories of resistance in cotton genotypes, Gossypium spp. against cotton-melon aphid, Aphis gossypii (Hemiptera: Aphididae).

Cotton-melon aphid, Aphis gossypii Glover (Hemiptera: Aphididae), is emerging as a potential threat to cotton cultivation worldwide. The resistance categories in Gossypium arboreum to A. gossypii still need to be explored. We screened 87 G. arboreum and 20 Gossypium hirsutum genotypes against aphids under natural field conditions. Twenty-six selected genotypes from these 2 species were tested under glasshouse conditions for resistance categories (antixenosis, antibiosis, and tolerance). Resistance categories were assessed by no-choice antibiosis assay, free-choice aphid settling assay, cumulative aphid days using population buildup tests, chlorophyl loss index, and damage ratings. No-choice antibiosis experiment revealed that the G. arboreum genotypes GAM156, PA785, CNA1008, DSV1202, FDX235, AKA2009-6, DAS1032, DHH05-1, GAM532, and GAM216 had a significant adverse effect on aphid development time, longevity, and fecundity. Gossypium arboreum genotypes CISA111 and AKA2008-7 expressed a low level of antixenosis but possessed antibiosis and tolerance. Aphid resistance persisted uniformly at different plant developmental stages studied. The chlorophyl loss percentage and damage rating scores were lower in G. arboreum than in G. hirsutum genotypes, indicating the existence of tolerance in G. arboreum to aphids. Logical relations analysis of resistance contributing factors depicted the presence of antixenosis, antibiosis, and tolerance in the G. arboreum genotypes PA785, CNA1008, DSV1202, and FDX235, indicating their utility for evaluating the mechanisms of resistance and aphid resistance introgression breeding into G. hirsutum to develop commercially cultivated cotton lines.

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses.

Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.