Vigna radiata (L.) Wilczek - ARCC Journals

Legume Research, , 40(4) 2017 : 601-608

AGRICULTURAL RESEARCH COMMUNICATION CENTRE

Print ISSN:0250-5371 / Online ISSN:0976-0571

www.arccjournals.com/www.legumeresearch.in

Review Article

Role of genomic tools for mungbean [Vigna radiata (L.) Wilczek] improvement Vijayata Singh1*, N.R. Yadav2 and Jogendra Singh1 Indian Council of Agriculture Research, Central Soil Salinity Research Institute, Karnal-132001, Haryana, India. Received: 17-10-2016 Accepted: 13-01-2017

DOI:10.18805/lr.v0i0.8406

ABSTRACT Molecular markers are routinely utilized worldwide in all major crops as a component of breeding. The pace of development of molecular markers, establishment of marker–trait associations for important agronomic traits and other genomic sources has been accelerated in other pulses than the mungbean. The efforts are underway to use high-throughput genotyping platforms besides developing more genomic resources. So far, progress in the use of marker-assisted selection as a part of mungbean breeding programmes has been very limited. In this article, we have reviewed the progress made, limitations encountered and future possibilities for the application of marker-assisted selection in the genetic improvement of mungbean crops. Key words: Mungbean, Molecular markers, Molecular breeding. Mungbean [Vigna radiata (L).Wilczek] is an important pulses crop in developing countries of Asia, Africa and Latin America, where it is consumed as dry seeds, fresh green pods (Karuppanapandian et al., 2006). On a dry-weight basis Mungbean contains 25 to 28% protein, 1.0 to 1.5% fats, 3.5 to 4.5% fibre, 4.5 to 5.5% ash and 60 to 65% carbohydrate. The seed protein is rich in lysine, but low in sulphur amino acids methionine and cystine. The seeds are also rich in ascorbic acid, vitamin A, potassium, iron, phosphorus and calcium, but low in sodium. Generally, mungbean provides an excellent complement for cerealbased diets, particularly in Asia where it used in various ways. Dried seeds are eaten whole or split, cooked, fermented or milled and ground into flour to make products like dal, soups, porridge, confections, curries and alcoholic beverages. The beans are popular for sprouting with major use as a fresh salad vegetable and vegetative parts of mungbean plant are used in fodder and green manure. It is an important source of an easily digestible with low flatulence protein as part of meal in the cereal based society. mungbean adapt well to various cropping systems owing to their ability to fix atmospheric nitrogen, N2 in symbiosis with soil bacteria, Rhizobium spp., rapid growth, and early maturity, therefore, trends on the demand and production of this crop is increasing day-by-day (Singh et al., 2005; Tomooka et al., 2005). It is native of India-Burma and is cultivated extensively in Asia (Khattak et al., 2007). India is the leading mungbean cultivator, covers near about 55% of the total world acreage and 45% of total production (Rishi, 2009). Being a short duration legume, (matured in 55 to 70 days),

mungbean fits well into many cropping systems, including rice and sugarcane, under both rainfed and irrigated conditions. Nevertheless, it has the capability of fixing atmospheric nitrogen, it improves soil condition and farmer’s conditions (Fernandez and Shanmugasundaram, 1988). India is the primary mungbean producer and contributes about 75 % of the world production. mungbean is the third most important pulse crop of India, after chickpea and pigeon pea. The national average of mungbean is 365 kg/ha. It is grown throughout the year in three crops season: Kharif (JulyOctober), rabi (September- December) and summer/spring (March-June). Indian society knows mungbean has a good nutritional value, but new information indicates it is even better than we expected. Mungbean is mostly neglected in the research programmes, both at national and international levels, particularly in the field of genomics. This is reflected by the fact that there have been less than two published papers per year on genome mapping in mungbean over the last 10 years. Considering, socioeconomic importance, we provide up to date review of genomic studies conducted on this crops in this review paper. ORIGIN, TAXONOMIC RELATIONSHIPS AND DIVERSITY OF CULTIVATED FORMS The genus Vigna is a large tropical genus consisting 82 described species distributed among 6 subgenera; Ceratotropis, Haydonia, Lasiospron, Plectotropis, Sigmoidotropis and Vigna. Ceratotopis has it centre of species diversity in Asia, consists 21 species of which eight

*Corresponding author’s e-mail: [email protected] 1 Chaudhary Charan Singh Haryana Agricultural University, Hisar-125004, Haryana, India.

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are domesticated including Moth bean [V. Aconitifolia (Jacq.) Maréchal], Azuki bean [V. angularis, (Willd.) Ohwi & Ohashi], Black gram [V. mungo (L.) Hepper], Mungbean [V. Radiata (L.)Wilczek], Creole bean [V. reflexo-pilosa Hayata var. glabra, Maréchal, Mascherpa & Stainer N. Tomooka & Maxted], Jungli bean [V.trilobata L. Verdc], Toapée, Thai [V. trinervia, Heyne & Wall Tateishi & Maxted] and Rice bean [V. umbellata, Thunb. Ohwi & Ohashi]. The most important domesticated species are mothbean, azuki bean, black gram and mungbean (Tomooka et al., 2006a). The information of genetic similarities and diversity among Vigna genotypes are necessary for breeding programs. The taxonomy of the genus Vigna has been primarily based on morphological attributes. Study results in a numerical taxonomic analysis showed a high level of genetic variation within the genus with a remarkably higher amount of variation associated with Vigna sp. from Africa relative to those from Asia. The distinctness of the Asiatic grams in subgenus Ceratotropis, cowpea in section Catiang, bambara groundnut, V. subterranean and members of the subgenus Plectotropis was elucidated by this study. Members of the subgenus Plectotropis were closer in genome homology to those of subgenus Vigna section Catiang than to those of subgenus Ceratotropis. The relative positions of some genotypes to one another on the dendrogram and minimum spanning tree were discussed in regard to hybridisations aimed generating well-saturated genomic maps and interspecies transfer of desirable genes (Fatokun, et.al 1993). GENOMIC TOOLS FOR MUNGBEAN IMPROVEMENT Genome organization: Mungbean is diploid in nature with 2n=2x=22 chromosome number. Mungbean has genome size estimated to be 0.60 pg/1C, 579 Mbp which are similar to those of the other Vigna species (Somta et al., 2007 & 2006), 46% of the single-copy DNA was interspersed within repetitive sequences at long periods greater than 6.7 kb. The repetitive sequence families covered a range of about 50 to several thousand copies per haploid genome. Duplicate markers were found on more than one linkage group with evidence of tandem duplication and other linkage arrangements of duplicated loci (Somta and Srinives, 2007). Molecular marker technologies and their utility: The development and use of biochemical-based analytical techniques and molecular marker technologies, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs) and microsatellites or simple sequence repeats (SSRs) have greatly facilitated the analysis of the structure of plant genomes and their evolution, including relationships among the Leguminoseae (Choi et al., 2004; Yan et al., 2004) based on their reproducibility, multi-allelic nature, co-dominant inheritance, relative

Fig 1: Gene pools of mungbean [Vigna radiata (L.)]: Gene pool 1: within which are the cultivated and wild forms of Mungbean. Gene pool 2: Less related species that can be artificially hybridized with Mungbean. Gene pool 3: Includes species from which gene transfer to mungbean is impossible that requires in vitro embryo rescue, radiation-induced break chromosome and somaclonal fusion. Source: (Tomooka et al., 2005).

abundance and good genetic coverage. This in turn has contributed significantly to our current understanding of the mungbean genome organization and evolution. Molecular markers are indispensable for genomic study. Not many genetic markers were developed specifically for mungbean or blackgram. Restriction fragment length polymorphism (RFLP) markers of both cDNA and random genomic clones of mungbean were reported (Young et al., 1992). These RFLPs together with those from common bean [Phaseolus vulagris (L.)], cowpea [V. Unguiculata L. Walps] and soybean [Glycine max (L.) Merr.] have been extensively used in mungbean and blackgram genome mapping (Somta et al.,2006). Only recently, microsatellite or simple sequence repeat (SSR) marker system have been developed from mungbean (Miyagi et al., 2004; Gwag et al., 2006). The number of these SSRs is still very limited. However, SSRs from common bean (Blair et al., 2003) and cowpea (Li et al., 2001) can be used in both mungbean and blackgram. 72.7% and 78.2% of the azuki bean SSRs amplify mungbean and blackgram genomic DNA, respectively. While 60.6% of common bean SSRs amplify mungbean genomic DNA (Chaitieng et al., 2006). Utility of marker technologies could be enunciated in following ways; Genetic linkage map: A high-density genetic linkage map with informative markers, is essential for plant genome analyses, such as gene mapping, identification of quantitative

Volume 40 Issue 4 (August 2017) trait loci, map-based cloning, and physical map construction. Now, F2 or recombinant inbred lines (RILs populations) based six molecular linkage maps for mungbean have been published (Menancio et al., 1993; Boutin et al., 1995; Lambrides et al., 2000; Humphry et al., 2002). A Linkage map form mungbean population developed from inter subspecific crosses of VC 3980, cultivated x TC1966, wild from Madagascar and Berken, cultivated x ACC41, wild from Australia have been published using RFLP and RAPD markers. The population size ranged from 58 to 80 plants. The maps differ in length (737.9-1570cM), number of markers (102-255 markers), number of linkage groups: 1214, level, 12-30.8% and regions of marker distortion. The most comprehensive map consists of 255 loci with an average distance between the adjacent markers of 3cM. However, none of the maps resolved 11 LGs, which is the haploid chromosome number of mungbean. To resolve 11 LGs and saturate the map, many more markers are needed. In addition, the genome coverage of the markers has yet to be determined. The genetic linkage map of mungbean, Vigna radiata, 2n = 2x = 22 was constructed (Zhao et al., 2010) using a recombinant inbred line, RIL population derived from an inter-sub specific cross between Berken, a bruchidsusceptible cultivar and ACC41, a bruchid-resistant genotype belonging to V. radiata subsp. sublobata. For enhancing the density of the existing linkage map, 104 pairs of polymorphic simple sequence repeat, SSR primer, were screened out. In combination with the data from other markers, a new genetic linkage map consisting of 179 markers was obtained (Kaga et al, 1998). They included 97 SSR markers, 91 of which were derived from mungbean close relatives, 76 RFLP markers, and 2 STS markers. These markers were assigned to 12 linkage groups with an average distance of 10.2 cM between markers. The transferability of the SSR markers from these relatives of mungbean, including azuki bean (V. Angularis), black gram (V. Mungo), common bean (Phaseolus vulgaris), and cowpea (V. Unguiculata) was also evaluated. Approximately 65% of SSR markers form azuki bean, 72% from black gram, 42% from common bean, and 30% from cowpea could be effectively amplified in Mungbean. These different ratios might reflect different levels of genomic homology between Mungbean and the four close relatives. A total of 98 pairs of polymorphic SSR primers from these close relatives were effective in genetic analysis of mungbean. The new linkage map of mungbean was compared with a published linkage map of azuki bean based on 32 common SSR markers. The majority of these markers were mapped in similar orders between these two species and a few markers with different orders suggested relative rearrangements between the two genomes. As previously reported, a major locus for bruchid resistance was located on linkage group 1. In this new map, the distances

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between the bruchid locus and its flanking markers were 8.0cM, C78 and 2.7cM, C220, respectively. Comparative genome mapping: Because all of the aforementioned mungbean linkage maps were developed by utilizing a number of heterologous probes from common bean, cowpea, lablab, Lablab purpureus and soybean. Comparative genomics, macro synteny was studied between mungbean and these legumes and the other Vigna species. mungbean and cowpea share a high degree of genome similarity. Marker orders and LGs were similar in both taxa with syntenic association appeared on 10 genomic regions although duplication and rearrangement exist (Menancio et al., 1993). Mungbean and azuki bean linkage maps share several conserved genome segments without or with some rearrangement (Kaga et al., 2000; Isemura et al., 2007) and showed that LG 1, 2, 3, 4, 8 and 11 of mungbean map (Menancio et al., 1993) correspond respectively to LG (1,4,10, 8, 2 and 9) of azuki bean map (Han et al., 2005). Genome conservation between mungbean and common bean appears to be higher than between mungbean and cowpea (Boutin et al., 1995) or azuki bean (Kaga et al., 2000). Comparison between mungbean and common bean or soybean maps revealed that mungbean genome is more conserved to common bean than soybean (Boutin et al., 1995). Linkage maps between mungbean and common bean showed extensive genome conservation average length of colinearity of 37cM with the maximum of 100cM but notable translocations in the genomes occurred as indicated by a mungbean LG was composted of different common bean LGs. While comparison between mungbean and soybean revealed that short, average colinearity length of 12-13cM and scattered linkage blocks are conserved and there are considerable genome rearrangements between the two species (Schmutz et al., 2010). A higher level of genome conservation between mungbean and soybean than previously reported (Lee et al., 2001). Comparative mapping in mungbean and a distantly related legume crop, lablab gave surprising results in that the two species share several large conserved genome blocks as indicated by similar marker orders and LGs (Humphry et al., 2002). However, the results also showed genome rearrangements and many deletions/duplications after divergence. In a recent study of genome conservation between a model legume Medicago truncatula and several other legume crops including mungbean using cross species genetic markers, the results showed that macro-syntenic relationship between M. Truncaluta and mungbean was complicated and less informative (Lee et al., 2001). Twentynine of 38, 76% markers used between the two taxa revealed evidence of conserved gene order, whereas the remaining markers mapped to non-syntenic positions.

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Advancements in Next-Generation Sequencing (NGS): With the advancement in NGS, researchers have focused on finding SNPs to be used as genetic markers, as SNPs are codominant, single-locus, bi-allelic markers that are abundant and ubiquitous throughout the genome and are readily used for genotyping (Brumfield et al., 2003). Moe et al. (2011) presented fundamental insights into functional annotation in the mungbean genome, including an overview of its gene content. Two varieties of mungbean,‘Seonhwanokdu’ (accession VC1973A) and ‘Jangannokdu,’ were subjected to 454 sequencing due to their respective susceptibility and resistance to stinkbug (Riptortus clavatus) and adzuki bean weevil (Callosobruchus chinensis). A total of 150, 159 and 142,993 reads were produced, generating 5,254 and 6,372 contigs greater than or equal to 500 bp, with an average length of 833 and 853bp for VC1973A and Jangannokdu, respectively. A total of 41.34 and 41.74% unigenes were functionally annotated to known sequences and classified into 17 and 18 Fun Cat functional categories for VC1973A and Jangannokdu, respectively, including metabolism, energy, cell cycle and DNA processing, transcription, protein synthesis, and so on.The authors then performed large-scale discovery of molecular markers : 1,334 (VC1973A) and 1,630 (Jangannokdu) microsatellite repeat motifs were counted, and 2,098 highly confident sequence variations wererevealed that could be utilized as SNP markers.These findings represent a valuable resource for functional genomics studies aimed at improving mungbean breeding efforts and increasing the marker density of linkage maps. In recent years, as sequencing has become increasingly popular due to the rapid development of NGS technologies, genome sequences have become available for crop species. Many instruments are used for high-through put sequencing, including SOLiD/ Ion Torrent PGM from Life Science, Genome Analyzer / HiSeq2000 / MiSeq from Illumina, and 454FLX Titanium /GS Junior by Roche (Liu et al., 2012). Until the early 2000s, when Illumina launched Illumina HiSeq 2000, mungbean SNPs were detected using 454GSFLX pyrosequencing. As Illumina HiSeq 2000 can be used to produce longer and more accurate contigs compared to Roche454 (Luo et al., 2012), Van et al. (2013) used this system for in silico identification of mungbean markers from two mungbean cultivars, VC1973A and Gyeonggijaerae5 (accession V2984); V2984 is susceptible to mungbean mottle virus, Cercospora leaf spot, and powdery mildew (Hong et al.,1983). The authors prepared a shotgun / paired-end library (500 bp insert) and sequenced more than 40.0 billion bp from both cultivars at a depth of 72x . After de novo assembly of contigs and alignment of VC1973A and V2984 reads, 265,001 homozygous SNPs were identified, 65.9% of which were transitions and 34.1% of which were transversions. To confirm the in silico SNPs, the common bean ESTs were mapped onto VC1973A contigs, revealing

approximately 80% sequence similarity between the two species (Schmutz et al., 2014). These findings represent a substantial molecular resource for developing a high-density genetic map and for examining genetic diversity in mungbean. An important milestone in Vigna genomic research was reached in 2014 with the completion of de novo sequencing of VC1973A, its polyploidy relative V. reflexopilosa var. Glabra (accession V1160), and its wild relative V. radiata var. Sublobata (accession TC1966), as well as the de novo assembly of RNA- seq data rom of 22 accessions of 18 Vigna species, facilitating advances in genomic research into the subgenus Ceratotropis and providing insights into the evolution with in Vigna species (Chen et al., 2015). Kang et al., (2014) sequenced the mungbean genome using Illumina HiSeq 2000 and GSFLX+, generating 2,748 scaffolds with an N50 length of 1.62 Mb on a 431Mb map (80% of the 579 Mb estimated genome size). Sequence analysis revealed 22,427 high-confidence protein-coding genes and 160 Vigna gene clusters. Furthermore, a high-density SNP link age map was constructed using 1,321 genotyping-by-sequencing (GBS) SNP markers covering all 11 linkage groups from F6 population of 190 recombinant inbred lines (RILs) based on across between VC1973A and the Korean landrace V2985. Previously, only low-resolution linkage maps were produced due to the limited number of available markers; however, the high-density genetic map produced in this study has an N50 length of 35.4 Mb, covering a physical length of 314Mb, which corresponds to 73% of the total mungbean genome. The domestication history of mungbean was traced by comparing sequence variants, such as SNPs and insertions / deletions (INDELs),in wild and cultivated Mungbean, especially non-synonymous SNPs in exonic regions related to domestication-related traits. Kang et al. (2014) compared wild and cultivated Mungbean genomes, revealing 2,922,833 SNPs at a frequency of 6.78 per kb. A total of 63,294 SNPs were detected in coding sequence (CDS) regions, 30,405 of which were non-synonymous, while 55,689 out of 342,853 INDELS were inserted / deleted bases located within genic boundaries caused by frameshifts in 1,057 genes. Kang et al. (2015) also prepared draft genome sequence of adzuki bean. A largeset of SSR markers (200,808 SSRs) will enhance future studies aimed at identifying the interaction between markers and QTLs, including those involved in biotic and abiotic stress responses. Translational genomics: Improvements in sequencing technology have led to the sequencing of the complete genomes of many crop species, which has opened the door for in-depth studies of structural and functional features, with the ultimate aim of crop improvement. Translational genomics tools have made plant breeding easier and more effective by enabling researchers and breeders to exchange genetic and genomic information among species (Gepts et

Volume 40 Issue 4 (August 2017) al., 2005; Stacey and Vanden Bosch, 2005). For example, the development of common legume markers has facilitated translational genomic studies in legume species, especially species lacking sequence information (Gepts et al., 2005). Therefore, translational genomics has also been referred to as genomics-assisted breeding (GAB; Varshney et al., 2005). Genome sequences are currently available for mungbean, but QTL mapping of this crop has not yet been reported. Comparative analysis between mungbean and soybean would assist mungbean QTL mapping, as SoyBase2 (the USDAARS soybean genetic database) contains over 1,000 QTL sequences for more than 90 agronomically important traits. Information from previously analyzed species can be utilized for other species, such as model systems to crops, a concept referred to as translational genomics (Varshney et al., 2015). Due to the completion of genome sequencing of several legume species, comparative analysis represents a powerful tool that can be used to support translational genomics studies. Using this technique, genomic knowledge (such as molecular markers) can be applied to crops that are poorly understood, ultimately leading to practical crop breeding and improvement strategies (Varshney et al., 2015). To conduct systematic translational genomic analysis, studies comparing the genome organization of model versus crop species are needed to supplement the available genomic data (Bordat et al., 2011). The potential of translational genomics has been revealed in early studies of legumes, as this technique benefits the analysis of less - studied crops. Based on sequence – based comparisons, Mudge et al. (2005) revealed orthologous and paralogous relationships of the genomic regions harboring soybean nematode resistance genes, rhg1 and rhg4, between soybean and Medicago truncatula. Moreover, large-scale comparisons between M. Truncatula and alfalfa were conducted to elucidate their syntenic relationships, chromosome relationships, and duplication histories (Cannon et al., 2006). Furthermore, several studies have focused on direct crop improvement in legume species based on information from well-studied plants. For example, Kwak et al. (2008) identified candidate genes responsible for determinacy and photoperiod Sensitivity traits in common bean (P. vulgaris) using homologs in Arabidopsis thaliana floral regulatory genes,and Yang et al. (2008) identified a putative resistance gene in alfalfa (M. sativa) based on map-based cloning of RCT1, a host resistance (R) gene in M. truncatula, which conferred resistance in alfalfa cultivars. Multiple-legume species macro synteny comparisons were also performed between cowpea and soybean,and cowpea and M. truncatula, based on the genetic map of cowpea.The availability of genome sequences across legume species including M. Truncatula (Young et al., 2011), Lotus japonicas (Sato et al., 2008), soybean (Schmutz et al.,2010), pigeonpea (Varshney et al.,2012), chickpea (Varshney et al.,2013), mungbean(Kang et

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al.,2014), commonbean (Schmutz et al.,2014), and adzuki bean(Kang et al.,2015) have enabled extensive comparative genomics across species, including genomic contents and gene orders. .For example, based on a search for reciprocal homologs among all pea gene sequences and genes from three sequenced legume species, M. truncatula, L. japonicas, and G. max, a total of 5,460 unigenes were positioned on the functional map. A detailed comparison of microsynteny among the species investigated revealed that a candidate gene for the hypernodulation mutation nod3 in pea is likely to be a homolog of Pub1, an M. Truncaluta gene involved in regulating nodulation (Bordat et al.,2011). In addition, soybean flowering genes were detected by searching for homologs of flowering regulatory genes in Arabidopsis (Jung et al., 2012), providing a framework for understanding soybean flowering, including flowering pathways and evolutionary mechanisms. Recent efforts to identify Mungbean flowering genes have been conducted through genome-wide comparative analysis of the 207 Arabidopsis genes known to be involved in flowering pathways,129 are homologous to mungbean genes, including five that area lsohomologous to soybean flowering genes (Kim et al., 2014). Moreover, some of these genes were localized close to SSR markers on a previous genetic linkage map by Isemura et al. (2012). This type of study enables researchers to uncover QTLs associated with specific traits. Based on sequence data from soybean and mungbean and QTLs from soybean1 controlling majoragronomic traits (Chen et al., 2007), putative mungbean QTLs were also identified. CONCLUSIONS AND FUTURE PERSPECTIVE Mungbean is still far behind in genomic research other than major legume crops such as soybean, cowpea, and common bean even than their relative but less important, azuki bean also. The fact that the current genetic linkage maps of mungbean not yet at detailed level, dense or saturated maps with 11 LGs resolved for the crops are needed. A major obstacle to achieve such maps is the lack of highthroughput SSR and SNP markers. As indicated above, the genome study in mungbean has been made possible by using genetic markers from other related legumes, and this trend will continue since only limited genetic resources are available for further study in mungbean. For example, SSRs from azuki bean, common bean and cowpea will be useful in development of mungbean linkage map with 11LGs resolved. Moreover, the information obtained from sequencing of soybean genome, common bean ESTs (Ramiirez et al., 2005) and M. truncatula and Lotus japonicas can create highthroughput genetic markers for mungbean. For the time being, information from a large number of soybean SSR and newly developed common bean SSR is worth investigating. In addition, a database of thousands of cowpea gene space sequences containing SSRs is now publicly available. With many genomic tools and resources for legumes are becoming increasingly available, a more detailed and in depth genome

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mapping of these two crops will be possible in the near future. By that time, genes or QTLs for important traits in the gene pool should be identified and located on genome maps such that marker-assisted selection can be practised for the crops. Another challenge for mungbean genome researchers is the development and establishment of a more efficient protocol of genetic transformation to support breeding work as the use of transgenic technology is inevitable for the crops in

the future. The technology will be helpful in development of micronutrient enrichment cultivars having biotic and abiotic stress. ACKNOWLEDGEMENTS Authors sincerely acknowledge the Department of Science and Technology, Govt. of India, New Delhi for providing INSPIRE Fellowship during Ph.D. research, due to this work was accomplished in smooth way.

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