The prevailing mono-cropping and intensive farming systems created the problem of several pests and diseases, and their intensive management through chemical measures has resulted in the development of resistance in pathogens against chemicals (Saxena et al., 2018). In India, biotic stresses including pests and diseases are reported to cause yield losses of up to 70% in black gram (Sharma et al., 2011), of which nearly 30% is due to insects (Justin et al., 2015). However, the avoidable losses due to pest incidence varied from 15.62% to 30.96% with an average of 24.03% in black gram production (Duraimurugan and Tyagi, 2014). It indicates that the loss due to the biotic stresses can be minimized through adopting resistant cultivars and integrated pest and disease management practices.

Among the abiotic stresses, drought, heat, waterlogging, and salinity stresses along with photo- and thermo-sensitivity are some of the major abiotic stresses responsible for severe yield losses in legumes across the production environment (Sultana et al., 2014; Nadeem et al., 2019). These stresses pose physiological changes to the plant and adversely affect the yield and nutritional quality of legume crops (Scheelbeek et al., 2018; Zonneveld et al., 2020). Black gram cultivation is performed year-round during rainy, post-rainy, and spring seasons across different agro-ecologies and cropping systems in India and other countries. In humid regions of North-East and coastal parts of India, black gram is grown soon after the monsoon rice crop to utilize the residual soil moisture, whereas it is grown as a rainfed crop in several parts of North India (Punjab, Haryana, Western Uttar Pradesh, and Bihar) (Singh et al., 2009). The water deficit stress is often experienced by the crop in many regions, especially during the rainfed and post-rainy season cultivation without supportive irrigation. Approximately 20%–30% of yield losses could be due to water deficit stress, which can be higher if the stress coincides with the flowering and pod development stage (Baroowa and Gogoi, 2012; Sai and Chidambaranathan, 2019; Kumar et al., 2020). It also reduces the efficiency of physiological processes such as the rate of photosynthesis and transpiration, and stomatal conductance (Durga et al., 2003; Baroowa and Gogoi, 2015). Moisture stress disturbs turgor pressure in the plant cells and affects cell enlargement, photosynthetic pigments, and membrane stability, resulting in poor plant growth. In addition to these, it also affects the stress response, defense systems of plants against pathogens, and several gene expressions and signaling pathways (Baroowa and Gogoi, 2015). The moisture deficit stress-tolerant varieties, viz., VBN4 and K1, showed a fivefold increase in production of abscisic acid (ABA) and lipid peroxidase activity compared to susceptible varieties (Sai and Chidambaranathan, 2019).

In several studies, the stress-tolerant black gram genotypes exhibited higher quantities of chlorophyll and increased leaf area index (Pratap and Sharma, 2010; Kumar et al., 2020), plant height, stress tolerance index, dry matter stress tolerance index, and assimilation rate (Baroowa and Gogoi, 2015; Yohan et al., 2018) compared to the reduction in these growth parameters in stress-susceptible genotypes (Gurumurthy et al., 2019; Shahi et al., 2019). Soil salinity reduces the chlorophyll content and affects leaf turgidity while increasing the production of proline (Ashraf, 1989).

The black gram is sensitive to low as well as higher temperature conditions. The high-temperature stress is responsible for the reduction of 38% to 82% of seed yield in black gram (Anitha et al., 2015). The pollen germination was significantly affected during higher temperatures. The plant traits such as leaf morphology (wax/pubescence), seed hardiness, pollen viability, and germination and receptivity of stigma were associated with temperature tolerance (Ganeshan et al., 2012; Choudhary et al., 2014). The higher temperature-tolerant (>38°C ± 2°C) genotype produced seed surface with shiny luster, thin and reduced cotyledon fissures, and bold and well-structured starch granules (Partheeban and Vijayaraghavan, 2020). Considering the changing climate scenario, breeding for climate-smart varieties that offer tolerance to prevailing biotic and abiotic stresses will ensure uninterrupted growth in genetic gains and supply of increasing future food demand.

Black gram shows a spreading plant type; however, the modern cultivars are developed with erect and semi-erect plant types. The erect plant type is not completely dominant over the spreading type (Sen and Jana, 1964). It has large trifoliate leaves that are either ovate or lanceolate in shape. Ovate leaf shape is dominant over lanceolate and is mainly controlled by a single dominant gene (Verma, 1971). However, the hastate shape is reported to be dominant over the ovate and probably controlled by duplicate dominant genes (Singh and Singh, 1971) ( Table 3 ). A fused leaf (cotton leaf type) variant was reported to be recessive to the ovate leaf shape and is controlled by a single recessive gene (Muralidharan et al., 1990). Two types of pod orientations, i.e., main stem bearing and sympodial bearing types, are found in black gram. Main stem pod bearing is controlled by a single incomplete dominant gene. Recently, the above canopy pod-bearing genotypes were also developed in black gram (Gupta et al., 2020). Three different pod colors are reported, viz., black, brown, and straw color, of which black pod color is very prominent and dominant over the straw and brown pod color (Sen and Jana, 1964; Verma, 1971; Arshad et al., 2005). The inheritance of protruded stigma and crumpled petals in naturally occurring mutants reported the involvement of a single recessive gene with a pleiotropic effect (Kumar et al., 2012). The brown seed coat color is recessive to the green seed coat color with qualitative inheritance (Sen and Jana, 1964). However, in contrast to this, brown seed coat color was reported to be dominant over green seed color by Arshad et al. (2005). Shiny seed surface is dominant over dull seed surface in black gram (Sen and Jana, 1964).

There are contrasting reports on the inheritance of resistance that include monogenic dominant (Dahiya et al., 1977; Kaushal and Singh, 1988a; Gupta et al., 2005; Gupta et al., 2013a), as well as the monogenic or digenic recessive nature of resistance to MYMD (Singh, 1981; Dwivedi and Singh, 1985; Verma and Singh, 1986; Singh et al., 1987; Pal et al., 1991; Rambabu et al., 2018) available in black gram. The duplicate and recessive epistatic gene interaction (Thamodhran et al., 2016) along with tri-genic control with inhibitory gene action (Vadivel et al., 2021) was also reported for resistance to MYMD. The chi-square goodness-of-fit test on an F₂ population revealed inhibitory gene action with two genes controlling the expression of resistance to MYMD (Subramaniyan et al., 2022). This suggests that the genetics of resistance to MYMD is complex, which could be due to the presence of different strains of the causal virus and their variable pathogenicity. Genetic analysis of resistance to PM reported it to be governed by a single recessive gene (Kaushal and Singh, 1989); however, a recent report indicates that the resistance is controlled by a single dominant gene without maternal effects (Santosh, 2016). The inheritance of resistance to CLS (Kaushal and Singh, 1991) and anthracnose is controlled by a single dominant gene (Kaushal and Singh, 1988b). Two duplicate dominant genes control resistance to bruchid (C. maculatus) infestation in black gram (Dongre et al., 1996; Souframanien and Gopalakrishna, 2007). However, resistance is also reported to be controlled by the monogenic dominant gene (Tickoo et al., 2006) ( Table 3 ).

As black gram originated in India, the largest number of its globally available genetic resources (3,146 accessions) are collected and conserved by the National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India (Singh D et al., 2016). The ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India, has the mandate of pulse crop improvement including black gram and also holds an active collection of approximately 829 accessions (Arora, 1988; Gupta et al., 2001). The largest black gram collection outside of India is held by the World Vegetable Center, Taiwan, comprising 884 black gram accessions that originated from different parts of the world (Jacob et al., 2015). Some other gene banks are holding black gram, viz., Plant Genetic Resources Centre (PGRC), Bangladesh Agricultural Research Institute (BARI), Bangladesh (339 accessions); Plant Genetic Resources Conservation Unit, University of Georgia, USA (304 accessions); N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Russia (220 accessions); and Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), Japan (220 accessions). Australian Grains Genebank, Australia (102 accessions) and International Center for Tropical Agriculture, Colombia (93 accessions) also hold black gram accessions ( Table 4 ). NARO has the largest number of accessions (14) of wild black gram. However, many germplasms conserved in several gene banks are duplicates of Indian origin. There is considerable genetic diversity available among the Indian black gram accessions (Singh et al., 1991; Singh and Shukla, 1994; Nautiyal and Shukla, 1999; Kaewwongwal et al., 2015); however, its exploitation was hindered by limited access to information about the germplasm such as characterization data and classification efforts (Gupta et al., 2001).

Molecular genetic diversity analysis of 520 cultivated and 14 wild accessions from various countries using 22 simple sequence repeat (SSR) markers revealed that the diversity of germplasm from different regions was comparable, albeit the germplasm from South Asia showed the greatest gene diversity (Kaewwongwal et al., 2015). The study also revealed that the level of gene diversity in black gram is close to that in mungbean and rice bean, but lower than azuki bean.

Black gram is classified into two sub-taxa, i.e., i) V. mungo var. mungo characterized by black large seeds and early maturity and the wild type ii) V. mungo var. silvestris Lukoki, Maréchal & Otoul, with denser inflorescences, hairier and climbing nature, and small seeds with prominent raised aril (Lukoki et al., 1980; Tomooka et al., 2000). V. mungo var. silvestris is considered to be the progenitor of cultivated black gram (Lukoki et al., 1980) and was successfully used in breeding programs for the genetic improvement of several traits (Jansen, 2006). Black gram is classified into the subgenus Ceratotropis (also known as Asian Vigna). Species in this subgenus are highly diverse and distributed widely in Asia (Tomooka et al., 2000), and thus, they adapt well to various environments and can be useful gene sources for the genetic improvement of black gram. Some of the important wild species of Vigna, namely, Vigna bourneae, Vigna capensis, Vigna dalzelliana, Vigna grandis, Vigna hainiana, Vigna minima, V. mungo var. sylvestris, Vigna radiata var. sublobata (wild mungbean), and Vigna vexillata, were collected from Western and Eastern Ghats, Northwestern Plains, Central Plateau region, and Northern Himalayas in India (Dana, 1998). Several accessions of wild Vigna species, i.e., Vigna aconitifolia, V. dalzelliana, V. hainiana, Vigna khandalensis, V. mungo var. silvestris, V. radiata var. sublobata, and Vigna trilobata, were collected from diversity rich areas of Gujarat, Rajasthan, Maharashtra, Madhya Pradesh, Bihar, Odisha, and West Bengal during 1974 and 1994 by NBPGR, New Delhi (Dana, 1998). However, there is no information on the cross-compatibility between a black gram and all of these wild Vigna species, except wild black gram and wild mungbean.

The cross-compatibility study of V. mungo with other species revealed 37.5% compatibility between V. radiata (♀) and V. mungo (♂), whereas it was 11.6% between V. mungo (♀) and Vigna umbellata (♂) (Bhanu, 2018). The true interspecific F₁’s among V. radiata (♀, SML 668 and SML 832) and V. mungo (♂, Mash 114 and Mash 218) reported 5.5% to 24.1% pod set, 14.29% to 30.56% germination, and 22.59% to 28.36% pollen fertility (Lekhi et al., 2018). Different kinds of pre- and post-fertilization barriers were responsible for complete sterility or low fertility in F₁ hybrids between these two species (Bhanu, 2018). Rice bean (V. umbellata) genotypes RBL 1 and RBL 9 showed high crossability and percent seed set with different cultivars of black gram. Another study successfully crossed V. mungo and V. radiata, and the recovered hybrids were reciprocally crossed with Vigna angularis. The reciprocal three-way interspecific F₁ hybrids were reported partially fertile (Gupta et al., 2002). The introgression of desirable traits from rice bean (RBL 1) into black gram (Mash 338 and UG 562 and 844) resulted in poor cross-compatibility and plant fertility for initial generations and improved gradually from the F₂ generation onward (Singh et al., 2013). The yield evaluation of 24 uniform F₇ progeny bulks exhibited −35.48% to 50.31% yield variation over the check cultivar (‘Mash 338’, a female parent) along with resistance to MYMD, CLS, and bacterial leaf spot diseases. The desirable traits such as a high number of pods per plant, seed weight, and MYMD resistance from rice bean have been successfully introgressed into the black gram.

Varieties Mash 1008 and Mash 118 released in 2004 and 2008, respectively, were developed from an interspecific cross between black gram and mungbean (Singh et al., 2016a). The variety Mash 114 was developed from an interspecific cross between black gram and rice bean and recorded a 39.45% superior yield over the check cultivar ‘Mash 338’ (female parent) across 14 multi-location trials (Singh et al., 2013). Another variety, Vamban 7, resistant to MYMD and powdery mildew was obtained from Vamban 3 × wild black gram (V. mungo var. silvestris), whereas TU-40, resistant to powdery mildew, was obtained from TU 94-2 × wild black gram (Singh et al., 2016a).

The efforts in characterization, evaluation, and screening of black gram germplasm for desirable traits identified several useful trait-specific genotypes for breeding programs. The trait-specific genotypes were identified as potential donors for some of the agronomic traits such as number of pods per plant (KL 1, UH 81-44, and IPU 99-79 with >150 pods), number of seeds per pod (IC 106088, HPU 193, HPU 2, and PLU 257 with >8 seeds per pod), early maturity (IPU96-3, IPU 31-5, PLU 710, L25-7, and STY 2848 <70 days), and MYMD resistance (IC 27026, IC 06088, UL 2, HPU 4, HPU188, STY 2848, UH 80-26, IP 99-127, PLU 62, PLU 158, and PLU227) (Gupta et al., 2001). JP219132 was reported to show extra-large seed size, leaves, and stems (Chaitieng et al., 2006; Naito et al., 2017).

Black gram germplasm identified for biotic stress resistance are compiled in Table 5 . The genotype LBG-645 was reported as highly resistant to powdery mildew in glass houses and laboratory screening (Priyanka et al., 2018). The genotypes CO-5, IPU 07-3, and Mash 1-1 exhibited moderate resistance to dry root rot compared to the susceptible check VO 2135-B-BL in sick pot assay (Elmerich et al., 2022). Cultivated black gram is known to be immune to Callosobruchus chinensis infestation but highly susceptible to C. maculatus (Srinives et al., 2007). However, wild progenitor V. mungo var. silvestris is resistant to C. maculatus with the larval antibiosis mechanism of resistance (Dongre et al., 1996; Tomooka et al., 2000). The genotypes that are resistant to spotted pod borer (Krishna et al., 2006) and stem fly were also reported in black gram (Neupane et al., 2021).

Black gram germplasm identified for abiotic stress resistance is summarized in Table 5 . Vamban 2 variety has been reported as tolerant to drought stress in different studies and hence could be used as a parent to develop new varieties and genetic populations to further investigate the mechanism of drought tolerance in black gram (Goyal and Khan, 2010; Solanki et al., 2011 and Singh et al., 2016b). Other genotypes such as PGRU 95016, COBG05, IPU 99209, IPU 941, and IPU 243 were also reported as drought tolerant (Gurumurthy et al., 2019). The black gram varieties ‘J.L’, ‘PDU-1’ (Dash and Shree, 2013), ‘VBG-07-001’, and ‘VBG-06-010’ (Partheeban, 2017) were found to perform well in high-temperature regimes. Gupta et al. (2021) studied a panel of 97 diverse black gram genotypes for yield under heat stress and non-stress conditions in the field and identified eight highly tolerant lines (‘UPU 85-86’, ‘IPU 94-2’, ‘IPU 98/36’, ‘NO-5731’, ‘PGRU 95014’, ‘PGRU 95016’, ‘PLU 1’, and ‘BGP 247’). The trait-specific genotypes for waterlogging tolerance (Rana et al., 2016), photo-insensitivity (Singh et al., 2016b; Dash and Shree, 2013), and thermo-insensitivity (Singh et al., 2016b; Partheeban, 2017) were reported in different studies and are listed in Table 6 .

Black gram germplasms that are useful for nutritional quality improvement are shown in Table 7 . The genotypes with high protein content such as LBG17, Malabiri local, Boudha local, and G. Udayagiri local with >25% protein (Kole et al., 2002) and K1 and IPU 11-02 with >24% protein content were identified in black gram (Rana et al., 2016). The genotypes UG-218 and HIM Mash were reported with better protein quality, especially high methionine and lysine content (Modgil et al., 2019). Accessions rich in iron (Fe) and zinc (Zn) were also reported in black gram, which could be used to develop biofortified varieties to achieve nutritional security by combating mineral malnutrition (Singh et al., 2017).

In India, the establishment of the All India Coordinated Pulses Improvement Project (AICPIP) in 1967 provided breeders access to improved germplasm and an opportunity to test their improved breeding lines in multi-location trials across the country. The collective efforts of State Agriculture Universities and the Indian Council of Agricultural Research-Indian Institute of Pulses Research (ICAR-IIPR) resulted in the development and release of over 85 black gram varieties. Before the establishment of AICPIP, the early efforts of varietal development resulted in the release of popular varieties such as T 9, T 27, and T 77 (Gupta et al., 2001). T 9, a selection from the material collected from Bareilly (UP) in the early 1950s, has been used extensively by different breeding programs (Goyal and Khan, 2010). The varieties T 9, ADT 1, and Co 1 had made significant contributions to black gram production in India and were extensively used in the breeding program as parents to develop new varieties (Gupta et al., 2001). In Myanmar, six varieties were developed and released to farmers including Yezin-2, Yenzin-3, Yenzin-5, Yezin 6, Yezin-7, and Pale Tun. The first four varieties were selected from accessions P-45-1 (India), P-11-30 (Myanmar), P-69-354 (Myanmar), and LBG-17 (India). Yezin-7 was developed from hybridization and selection of the cross Yezin-4 and Yezin-6. Pale Tun is a mutant of P-11-30. In Thailand, farmers, traders, and users prefer varieties with large seed sizes. U-Thong 2 and Phitsanulok 2, pure-line varieties selected from Indian varieties 68/71 and BC48 (PI 288603) and released in the late 1970s and early 1990s, respectively, have been grown widely by the farmers for nearly 25 years due to high and stable yield and large seed size, compared to local varieties. At present, Chai Nat 80, a progeny derived from hybridization between a local variety (Prajeen) and an Indian variety (NBG 5), is the most popular cultivar in Thailand. In Australia, Regur released in the mid-1970s has been grown as a single black gram variety for approximately 35 years. The list of varieties developed in India, Bangladesh, Pakistan, Thailand, Australia, and Myanmar is presented in Table 8 .

In India, over 60% of black gram varieties share type 9 (T9) as one of the ancestors in their pedigree (Singh et al., 2016a). The pedigree analysis of advanced breeding lines entered for the Initial Varietal Trial in AICPIP from 1996 to 2005 revealed that T9 was used as one of the parents in over 78% of the advanced breeding lines (Katiyar et al., 2008). Another variety, D 6-7, was used as a parent in more than 12% of advanced breeding lines. The use of the limited number of parents by the breeding programs could be one of the reasons behind the narrow genetic base of available varieties. Therefore, it is an urgent need for the breeding programs to focus more on the use of diverse genetic material and recycling the newly developed advanced breeding lines into crossing nurseries.

Genetic improvement in several food legumes by either traditional or molecular approaches has been hindered due to the absence of genomic resources till the last decade (Varshney et al., 2009). The DNA marker techniques have been developed in various crops including food legumes owing to the recent developments in molecular biology. It includes the development of several different generations of molecular markers, molecular characterization of germplasm, and the development of genetic and quantitative trait locus (QTL) maps along with trait-linked diagnostic markers (Boukar et al., 2019). Genetic linkage maps and diversity within germplasm collections in black gram have been studied primarily using random amplified polymorphic DNA (RAPD) (Souframanien and Gopalakrishna, 2004), inter simple sequence repeat (ISSR) (Souframanien and Gopalakrishna, 2004), amplified fragment length polymorphism (AFLP), and SSR markers (Chaitieng et al., 2006).

Several efforts have been made to develop genomic resources and use them to assess the diversity at the genomic level in black gram. The DNA polymorphism in 18 elite genotypes using 25 RAPD and 16 ISSR markers reported 44 out of 104 scoreable fragments for RAPD and 55 out of 101 bands for ISSR as polymorphic (Souframanien and Gopalakrishna, 2004). ISSR markers have been effectively used for repeat motif analysis as well as varietal identification in black gram (Ranade and Gopalakrishna, 2001). The genetic diversity of 26 black gram landraces using AFLP markers revealed 74.5% to 93% polymorphism (Sivaprakash et al., 2004).

Since there were not many polymorphic markers in black gram, the transferability of SSR markers from other Vigna species to a black gram was tested and reported several polymorphic markers. Chaitieng et al. (2006) tested the amplification and polymorphism of 211 genomic SSR markers from azuki beans in cultivated and wild black and found that 73% and 50% of the markers were amplifiable and polymorphic, respectively. Chankaew et al. (2014) analyzed the application of 1,429 azuki bean genic SSR markers in the same black gram accessions used by Chaitieng et al. (2006) and found that 84% of the markers were amplifiable but that only 13% of them were polymorphic. Tangphatsornruang et al. (2009) detected amplification and polymorphism of 127 mungbean genomic SSR markers in cultivated and wild black gram and found that 66% and 50% of the markers were amplifiable and polymorphic, respectively. In a similar study, Somta et al. (2009) reported that as high as 92% of 85 genic SSR markers from mungbean tested in the same black gram materials reported by Tangphatsornruang et al. (2009) were amplifiable and 34% were polymorphic. Sixty-five SSR markers of cowpea were tested across different Vigna species and reported amplification of 85% (55) markers in black gram (Gupta and Gopalakrishna, 2010). The molecular diversity of six MYMD-resistant and MYMD-susceptible genotypes each from mungbean and black gram using 24 cowpea resistance gene analog (RGA) markers grouped two resistant (IPU 02-33 and IPU 6-02) and two susceptible (LBG 20 and T9) black gram genotypes into distinct clusters (Narasimhan et al., 2010). However, the limited number of SSR markers in these legumes hindered the genomic studies in the black gram.

The emergence of advanced sequencing technologies including next-generation sequencing (NGS) and third-generation sequencing (TSG) in the 2000s has revolutionized genome study in living organisms. NGS is able to sequence millions of short fragments of DNA in parallel. It provides a rapid, inexpensive, and comprehensive analysis of the genomes of individual organisms as well as complex populations. NGS is also a powerful tool in the discovery and genotyping of large numbers of single-nucleotide polymorphisms (SNPs) at a drastically reduced expense (Elshire et al., 2011) and in the construction of whole-genome sequencing, thus enhancing the genetic gain in breeding. Third-generation sequencing (TGS) (also known as single-molecule sequencing) sequences large numbers of long fragments of DNA, which is highly useful for producing high-quality genome assemblies providing scientists to explore genomes at an unprecedented resolution. The transcriptome sequencing of immature seed tissues of TU94-2 through Illumina paired-end sequencing technology generated 17.2 million paired-end reads and 48,291 transcript contigs (TCS) that could be useful for gene discovery and genic-SSR markers (Souframanien and Reddy, 2015). Another study on the transcriptome sequence of immature seed tissue in wild black gram developed a large number of genic SSR and SNP markers (Raizada and Souframanien, 2019). Genetic relatedness among 27 black gram genotypes was also evaluated using 19 genic SNPs through high-resolution melt (HRM) analysis (Raizada and Souframanien, 2021).

A whole-genome sequence (WGS) or reference genome sequence of a species is an indispensable genomic resource for gene discovery. WGSs of black grams have been developed recently. Pootakham et al. (2020) produced a high-quality, chromosome-level assembly of 499 Mb comprising 11 pseudomolecules from the black gram variety Chai Nat 80 (CN80) using NGS and TGS technologies. The genome annotation contained 32,729 predicted gene models, of which 29,411 (89.86%) were protein-coding genes. Shortly, Souframanien et al. (2021) constructed a draft genome sequence of 502 Mb of black gram variety Pant U-31 with 42,115 predicted genes. Ambreen et al. (2022) constructed a draft reference-guided genome assembly of black gram genotype ‘Uttara’ (IPU 94-1; known for its high resistance to Mungbean Yellow Mosaic Disease), with a cumulative size of 454 Mb and 28,881 predicted genes, of which 444 Mb was anchored on 11 chromosomes. Naito et al. (2022) constructed a draft genome sequence of 475 Mb of black gram variety Subsmotod with 28,227 predicted genes. The size of these black gram genome assemblies is only 79%–87% of the estimated genome size of the black gram (574 Mb; Arumuganathan and Earle, 1991). Therefore, a large part of the black gram genome still cannot be captured. In addition, the number of predicted genes in these genomes is highly different, albeit this may reflect the high genome variations among the black gram varieties. Nonetheless, these WGSs are useful genomic resources to hasten the understanding of evolutionary relationships, the development of diagnostic molecular markers, and the identification of novel genes and haplotypes in black gram.

The development of genomic resources opens opportunities for the construction of linkage maps and the identification of quantitative trait loci and diagnostic molecular markers for desirable traits (He et al., 2014). High-quality genome assembly together with information about genomic variations from germplasm enabled the use of novel breeding tools such as genomic selection (GS), marker-assisted selection (MAS), marker-assisted recurrent selection (MARS), and marker-assisted backcrossing (MABC) (Ribaut et al., 2010) and further comparative genomics and phylogenetic research into legumes (Pandey et al., 2016). Due to limited genomic resources for the black gram, especially polymorphic DNA markers, in the past, there have been few reports on gene and QTL mapping in this crop. A genetic linkage map is a basic tool for gene and QTL mapping. The first genetic linkage map of the black gram was reported in 2006 when Chaitieng and her colleagues developed linkage maps for the black gram using only 148 marker loci including 59 RFLP, 61 SSR, 27 AFLP, and one morphological marker (Chaitieng et al., 2006). Two years later, another black gram linkage map was developed using 428 marker loci (254 AFLP, 86 RAPD, 41 ISSR, and 47 SSR markers), but unfortunately, most of them were dominant (Gupta et al., 2008). Recently, a high-density linkage map of 3,675 SNP markers from specific-locus amplified fragment sequencing was developed (Somta et al., 2019). All of these maps were constructed based on a population derived from crossing between cultivated and wild black gram.

Most of the gene and QTL mapping studies in black gram involved the resistance to MYMD and bruchid (C. maculatus). By using bulked-segregant analysis (BSA), Gupta et al. (2013b) identified SSR marker CEDG180 linked to MYMD resistance. ISSR marker ISSR8111357 was identified to be linked to the MYMD resistance gene with a 6.8-cM distance, and the marker was converted into sequence characterized amplified region (SCAR) marker for validation on other MYMD resistant and susceptible genotypes (Souframanien and Gopalakrishna, 2006). Through BSA using an F₂ population of a cross between T9 (MYMD resistant) and LBG-759 (MYMD susceptible), SSR marker VR9 was found to be linked to MYMD resistance (Naik et al., 2017). In another study, SSR marker CEDG185 was identified as linked with the MYMD resistance by BSA (Rambabu et al., 2018). Two major QTLs, qmymv2_60 and qmymv10_60, governing resistance to MYMD disease were mapped onto LG2 and LG10 with 20.90% and 24.90% phenotypic variation explained (PVE), respectively (Vadivel et al., 2021). Validation of these QTLs in two other mapping populations confirmed the presence of qmymv10_60. Similarly, a study on the F₂ population derived from a cross between MDU 1 (susceptible) and TU 68 (resistant) identified one major QTL qMYMVD_60 on LG10 responsible for 21% PVE of MYMD variation. This QTL was delimited by SSR markers CEDG180 and CEDG116 (Subramaniyan et al., 2022). Since the QTL qmymv10_60 was confirmed and validated for its association with MYMD resistance in different studies, this QTL can be one of the potential regions for fine mapping and identification of diagnostic markers and haplotypes for MAS and haplotype-based breeding approaches.

By utilizing the genetic map developed by Gupta et al. (2008) (see above), QTLs Cmrae1.1 and Cmrae1.2 on LG3 and LG4, respectively, were detected for the percent adult emergence, and six QTLs (two (Cmrdp1.1 and Cmrdp1.2) on LG1, three (Cmrdp1.3, Cmrdp1.4, and Cmrdp1.5) on LG2, and one (Cmrdp1.6) on LG10) were identified for developmental period with PVE ranging from 8.4% to 16.4% (Souframanien et al., 2010). By using the high-density SNP-based linkage map, two QTLs, qVmunBr6.1 and qVmunBr6.2, located approximately 10 cM apart on LG6 were identified for a percentage of damaged seeds and infestation severity progress (Somta et al., 2019). Comparative genome analysis revealed qVmunBr6.1 and qVmunBr6.2 as new loci for C. maculatus resistance in Vigna species (Somta et al., 2019).

QTLs for seed weight were detected in black gram using mog (multiple-organ gigantism) mutant as the large-seeded parent. The mog mutant expressed extra-large size of seeds, leaves, and stems. QTL mapping and gene transformation studies revealed that mog gene accounted for approximately 66% of seed weight variation in the mapping population and additive gene effect of the mog increased 2.0 g of seed weight and that mog is a VmPEAPOD (VmPPD) gene (Naito et al., 2017). Loss of function caused by an 8-bp deletion on the VmPPD resulted in the mog phenotype (Naito et al., 2017). Later, major QTLs for the multiple-organ gigantism (MOG) phenotypes were reported on LG6 with the pleiotropic effect on different traits ranging from 15% for plant height to 40% for leaf size (Somta et al., 2020). The QTL for the MOG phenotype was also reported to contribute approximately 30% PVE for seed weight (Somta et al., 2020). In another study, QTLs for seed weight were identified using two F₂ populations derived from crossing between cultivated and wild black grams in which 10 QTLs on seven linkage groups (LGs) were detected in total for the seed weight (Lomlek et al., 2023). The QTLs explained between 5.07% (qSd100wt7.1+) and 34.20% (qSd100wt10.2+) of the weight variation, depending on the population. Genes encoding for pentatricopeptide repeat (RPP)-containing protein, WRKY46, glutathione S-transferase U9, NAC domain-containing protein 100, calcineurin B-like protein (CBL)-interacting protein kinase, cyclin-D6-1, kinesin, histidine phosphotransfer protein, AUXIN RESPONSE FACTOR 2A, and WAVE-DAMPENED2 (WVD2)-like 4 protein are candidate genes for seed weight QTLs (Lomlek et al., 2023). Two minor QTLs for pod dehiscence, qPdt3.1− and qPdt5.1−, on LGs 3 and 5, respectively, with ≤10% PVE and a single QTL with large effect controlling approximately 20% PVE for seed dormancy were also reported in black gram (Somta et al., 2020). The QTLs detected for pod dehiscence in black gram were different than those reported in other closely related Vigna species including mungbean (Isemura et al., 2012), adzuki bean (Kaga et al., 2008), moth bean (Yundaeng et al., 2019), and cowpea (Kongjaimun et al., 2012). Recently, QTL analyses using dense SNP-based linkage maps of two mapping populations identified 12 different QTLs with PVE of 3.4% to 38.0% for flowering time in the black gram (Suamuang et al., 2023). Genes encoding zinc finger protein 10, F-box protein SKIP14, and NAC domain-containing protein 37-like are candidate genes at major QTLs for the flowering time (Suamuang et al., 2023). None of the candidates are the same as those for flowering time in other Vigna species. In addition, using the same populations and linkage maps as that reported by Suamuang et al. (2023), 10 QTLs were detected for seed weight, and three were detected for seed dormancy. Depending on populations, QTLs explained between 5.07% (qSd100wt7.1+) to 34.20% (qSd100wt10.2+) of the seed weight variation and 10.18% (qSdwa6.1−) to 43.81% (qSd100wt6.2−) of the seed dormancy variation (Lomlek et al., 2023). Several candidate genes were identified including WVD2-LIKE 4 for seed weight that appeared to be an ortholog with a candidate gene for the seed weight in mungbean.