Multi-GWAS reveals significant genomic regions for Mungbean yellow mosaic India virus resistance in urdbean (Vigna mungo (L.) across multiple environments.

KEY MESSAGE: Unraveling genetic markers for MYMIV resistance in urdbean, with 8 high-confidence marker-trait associations identified across diverse environments, provides crucial insights for combating MYMIV disease, informing future breeding strategies. Globally, yellow mosaic disease (YMD) causes significant yield losses, reaching up to 100% in favorable environments within major urdbean cultivating regions. The introgression of genomic regions conferring resistance into urdbean cultivars is crucial for combating YMD, including resistance against mungbean yellow mosaic India virus (MYMIV). To uncover the genetic basis of MYMIV resistance, we conducted a genome-wide association study (GWAS) using three multi-locus models in 100 diverse urdbean genotypes cultivated across six individual and two combined environments. Leveraging 4538 high-quality single nucleotide polymorphism (SNP) markers, we identified 28 unique significant marker-trait associations (MTAs) for MYMIV resistance, with 8 MTAs considered of high confidence due to detection across multiple GWAS models and/or environments. Notably, 4 out of 28 MTAs were found in proximity to previously reported genomic regions associated with MYMIV resistance in urdbean and mungbean, strengthening our findings and indicating consistent genomic regions for MYMIV resistance. Among the eight highly significant MTAs, one localized on chromosome 6 adjacent to previously identified quantitative trait loci for MYMIV resistance, while the remaining seven were novel. These MTAs contain several genes implicated in disease resistance, including four common ones consistently found across all eight MTAs: receptor-like serine-threonine kinases, E3 ubiquitin-protein ligase, pentatricopeptide repeat, and ankyrin repeats. Previous studies have linked these genes to defense against viral infections across different crops, suggesting their potential for further basic research involving cloning and utilization in breeding programs. This study represents the first GWAS investigation aimed at identifying resistance against MYMIV in urdbean germplasm.

Effect of herbicide stress on synchronization of carbon and nitrogen metabolism in lentil (Lens culinaris Medik.).

Weed invasion causes significant yield losses in lentil. Imazethapyr (IM), a broad-spectrum herbicide inhibits the biosynthesis of branched chain amino acids necessary for plant growth. Plant growth depends upon translocation of photo-assimilates and their partitioning regulated by carbon and nitrogen metabolism. This study aimed to investigate the impact of imazethapyr spray on carbon and nitrogen metabolism in tolerant (LL1397 and LL1612) and susceptible (FLIP2004-7L and PL07) lentil genotypes during vegetative and reproductive development. Significantly higher activities of invertases and sucrose synthase (cleavage) in leaves and in podwall and seeds during early phase of development in tolerant genotypes were observed as compared to susceptible genotypes under herbicide stress that might be responsible for providing hexoses required for their growth. Activities of sucrose synthesizing enzymes, sucrose phosphate synthase and sucrose synthase (synthesis) increased significantly in podwalls and seeds of LL1397 and LL1612 genotypes during later phase of development towards maturity while the activities decreased in FLIP2004-7L and PL07 genotypes under herbicide stress. Activities of nitrate and nitrite reductase, glutamine 2-oxoglutarate aminotransferase, glutamine synthetase and glutamate dehydrogenase were increased in leaves, podwalls and seeds of LL1397 and LL1612 under herbicide stress. A proper synchronization of carbon and nitrogen metabolism in tolerant lentil genotypes during vegetative and reproductive phase might be one of the mechanisms for their recovery from herbicide stress. This first ever comprehensive information will provide a basis for future studies on the molecular mechanism of source sink relationship in lentil under herbicide stress and will be utilized in breeding programmes.

Impact of post-emergent imazethapyr on morpho-physiological and biochemical responses in lentil (Lens culinaris Medik.).

Yield reduction in lentil crop due to weed infestation is a key hindrance to its growth due to poor weed-crop competition. Imazethapyr (IM), a selective herbicide, target acetolactate synthase (ALS) which catalyzes the first reaction in biosynthesis of branched chain amino acids, required for plant growth and development. The objective of the present study was to investigate the impact of IM treatment on weeds, ALS enzyme activity, antioxidant capacity, osmolyte accumulation, growth and yield related parameters in lentil genotypes. Two IM tolerant (LL1397 and LL1612) and two susceptible (FLIP2004-7L and PL07) lentil genotypes were cultivated under weed free, weedy check and IM treatments. Weed control efficiency reached its peak at 21 days after spray (DAS). Imazethapyr treatment decreased chlorophyll and carotenoid content up to 28 DAS with higher reduction in susceptible genotypes. FLIP2004-7L and PL07 had reduced plant height and lower number of pods under IM treatment which resulted in decreased seed yield. Higher ALS activity in LL1397 and LL1612 at 21 DAS, higher antioxidant capacity and glycine betaine content both at 21 and 28 DAS and lower decrease in relative leaf water content might be mediating herbicide tolerance in these genotypes that led to higher seed yield. The identified IM tolerance mechanism can be used to impart herbicide resistance in lentil. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01244-x.

A large-effect QTL introgressed from ricebean imparts resistance to Mungbean yellow mosaic India virus in blackgram (Vigna mungo (L.) Hepper).

KEY MESSAGE: Here, we report identification of a large effect QTL conferring Mungbean yellow mosaic India virus resistance introgressed from ricebean in blackgram variety Mash114. The tightly linked KASP markers would assist in marker-assisted-transfer of this region into Vigna species infected by MYMIV. Until recently, precise location of genes and marker-assisted selection was long thought in legumes such as blackgram due to lack of dense molecular maps. However, advances in next-generation sequencing based on high-throughput genotyping technologies such as QTL-seq have revolutionized trait mapping in marker-orphan crops. Using QTL-seq approach, we have identified a large-effect QTL for resistance to Mungbean yellow mosaic India virus (MYMIV) in blackgram variety Mash114. MYMIV is devastating disease responsible for huge yield losses in blackgram, greengram and other legumes. Mash114 showed consistent and high level of resistance to MYMIV since last nine years. Whole genome re-sequencing of MYMIV-resistant and susceptible bulks derived from RILs of cross KUG253 X Mash114 identified a large-effect QTL (qMYMIV6.1.1) spanning 3.4 Mb on chromosome 6 explaining 70% of total phenotypic variation. This region was further identified as an inter-specific introgression from ricebean. Linkage mapping using KASP markers developed from potent candidate genes involved in virus resistance identified the 500 kb genomic region equaling 1.9 cM on genetic map linked with MYMIV. The three KASP markers closely associated with MYMIV originated from serine threonine kinase, UBE2D2 and BAK1/BRI1-ASSOCIATED RECEPTOR KINASE genes. These KASPs can be used for marker-assisted transfer of introgressed segment into suitable backgrounds of Vigna species.

Genome-wide Association Study for Yield and Yield-Related Traits in Diverse Blackgram Panel (Vigna mungo L. Hepper) Reveals Novel Putative Alleles for Future Breeding Programs.

Blackgram (Vigna mungo L. Hepper) is an important tropical and sub-tropical short-duration legume that is rich in dietary protein and micronutrients. Producing high-yielding blackgram varieties is hampered by insufficient genetic variability, absence of suitable ideotypes, low harvest index and susceptibility to biotic-abiotic stresses. Seed yield, a complex trait resulting from the expression and interaction of multiple genes, necessitates the evaluation of diverse germplasm for the identification of novel yield contributing traits. Henceforth, a panel of 100 blackgram genotypes was evaluated at two locations (Ludhiana and Gurdaspur) across two seasons (Spring 2019 and Spring 2020) for 14 different yield related traits. A wide range of variability, high broad-sense heritability and a high correlation of grain yield were observed for 12 out of 14 traits studied among all environments. Investigation of population structure in the panel using a set of 4,623 filtered SNPs led to identification of four sub-populations based on ad-hoc delta K and Cross entropy value. Using Farm CPU model and Mixed Linear Model algorithms, a total of 49 significant SNP associations representing 42 QTLs were identified. Allelic effects were found to be statistically significant at 37 out of 42 QTLs and 50 known candidate genes were identified in 24 of QTLs.

Methylglyoxal detoxification pathway - Explored first time for imazethapyr tolerance in lentil (Lens culinaris L.).

Lentil is an important pulses crop but it's short stature and slow growth rate make it vulnerable to weed competition, limiting crop productivity. There is need to identify herbicide tolerant genotypes and their tolerance mechanism. The present investigation was conducted to understand the effect of imazethapyr (IM) treatment on accumulation of methylglyoxal (MG) and its detoxification mechanism in IM-tolerant (LL1397 and LL1612) susceptible (FLIP2004-7L and PL07) genotypes sown under control (weed free), weedy check (weeds were growing with crop) and sprayed with imazethapyr. The enzymes of glyoxalase pathway (glyoxalase I, II and III) and non glyoxalase pathway (methylglyoxal reductase), lactate dehydrogenase (LDH), glutathione content, gamma-glutamyl-cysteine synthetase (γ-GCS) were estimated in lentil genotypes at different days after spray. Higher activities of glyoxalase I, II and III and MGR along with the increased glutathione content (GSH) content in LL1397 and LL1612 under IM treatment as compared to FLIP2004-7L and PL07 might be responsible for lowering MG accumulation and increasing lactate content, which is end product of these pathways. Enhanced LDH activity in LL1397 and LL1612 might be responsible for energy production via TCA cycle that might be responsible for growth and recovery of tolerant genotypes after IM treatment. Higher γ-GCS activity in tolerant genotypes led to increased glutathione content required for glyoxalase pathway. However, decreased activities of glyoxalase enzymes and MGR in susceptible genotypes result in MG accumulation which limit plant growth. This is the first ever study elucidating the role of MG detoxification pathway conferring IM tolerance in lentil.

Insights into carbon and nitrogen metabolism and antioxidant potential during vegetative phase in quinoa (Chenopodium quinoa Willd.).

The present investigation was carried out to understand the impact of carbon and nitrogen metabolism in quinoa genotypes IC411824, IC411825, EC507747 and EC507742 during pre-anthesis stage. It was observed that activities of acid invertase, sucrose synthase (cleavage) and sucrose phosphate synthase (SPS) increased up to 75 days after sowing (DAS) and this might be responsible for providing reducing sugars for the development of vegetative parts. Enhanced activities of nitrate reductase, glutamate synthase, glutamine synthetase during vegetative growth of leaves and stem at 90 DAS assist the fixation of ammonia on glutamate molecule to synthesize amino acids at early stages. However, the glutamate dehydrogenase and nitrite reductase play a central role in the re-assimilation of amides from the amino group of asparaginase. As a result, these photosynthetic products will be responsible for providing both the energy and the C-skeletons for ammonium assimilation during amino acid biosynthesis. Leaves and stem of IC411824 and IC411825 had higher total phenol and total flavonoid content. DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity was found to be higher in leaves of IC411825 and in stem of IC411824 and IC411825 indicating their capability to act as natural antioxidants.