​Advances in Molecular Breeding for Bruchid (Callosobruchus spp.) Resistance in Mungbean [Vigna radiata (L.) Wilczek]: A Review

Mungbean is one of the most important grain legumes with high-quality dietary protein in India as well in many other Asian countries. But the crop is severely affected by bruchids (Callosobruchus spp.) from field to storage condition. These storage pests not only affect the yield but also reduce the market value and quality of the crops. The chemical method of bruchid management is not economical and environmentally unsafe. So, the host-plant resistance to bruchids would be the best alternative and most sustainable way to control the bruchid. A very limited number of wild accessions and cultivated genotypes are available for the transfer of bruchid resistance gene through conventional breeding. Thus, insights into the molecular mechanism of resistance will help to find out the resistance genes/QTLs easily with the support of available genome sequence and that can be introgressed to the cultivated varieties through marker-assisted backcross breeding (MABB) approach. Therefore, in this review, we focused on QTL mapping, identification of novel QTLs, marker assisted-selection, genomics and transcriptomics study by using advanced molecular tools which will be very helpful for genomic-assisted breeding in mungbean for bruchid resistance.

Stacking of Pup1 QTL for Low Soil Phosphorus Tolerance and Bacterial Blight Resistance Genes in the Background of APMS6B, the Maintainer Line of Rice Hybrid DRRH-3

Phosphorus (P) is one of the macro nutrients essential for plant growth and development. Rice (Oryza sativa L.) is sensitive to P starvation and its deficiency influences many key plant functions which results in crop yield penalty. Although the hybrid rice segment is well-known for its yield heterosis, P deficiency and bacterial leaf blight (BLB) diseases are the evident limitations. APMS6B, the female parent of DRRH-3 is susceptible to low P and bacterial blight disease. In the present study, the improvement of APMS6B to P starvation and resistance to bacterial leaf blight (BB) was carried out using marker-assisted backcross breeding (MABB) approach. Kasalath (+ Pup1 QTL) was used as donor and a promising IL (ATR 594-1) at BC1 F4 generation was identified with 81.15% RPGR. Concurrently, this IL was intercrossed with GU-2 (+ Xa21 and Xa38 ). Hybridity of Intercross F1s (ICF1) was confirmed through foreground selection having maximum RPGR (88.29%) and were selfed to produce ICF2. The resultant progenies were phenotyped for BB using Xoo inoculum (IX-020), simultaneously genotyped with gene specific functional SSR markers for Xa21 and Xa38. The identified BB resistant plants were subjected to foreground selection for Pup1. Four promising ICF3 plants (BP-10-1, BP-10-3, BP-10-5 and BP-10-15 with Xa21, Xa38 and Pup1) along with parents and checks were screened both in low P plot (<2 kg P2O5 ha-1 ) as well as in normal plot (>25 kg P2O5 ha-1) during dry and wet seasons 2018. Based on the field evaluation, four promising intercrossed lines were identified with better root architecture in terms of root length and root volume. In addition, less % reduction in grain yield (39.10%) under P starvation and less susceptibility indices values (<1) for BB were observed. These lines may be utilized in the CMS conversion programme and development of climate resilient, biotic and abiotic tolerant rice hybrids.

Marker-Assisted Pyramiding of Downy Mildew-Resistant Gene Ppa3 and Black Rot-Resistant Gene Xca1bo in Popular Early Cauliflower Variety Pusa Meghna

Cauliflower is an important extensively grown cool season vegetable in India. Black rot and downy mildew are major devastating diseases reducing yield and quality of the crop. To tackle these through host plant resistance, a marker-assisted backcross breeding method was followed to pyramid a black rot-resistant gene (Xca1bo) and a downy mildew-resistant gene (Ppa3) from donors BR-161 and BR-2, respectively, into the background of Pusa Meghna cauliflower cultivar. Marker-assisted backcross breeding was followed up to BC2 generation using SCAR marker ScOPO-04833 and SSR marker BoGMS0624 for black rot and downy mildew resistance genes in foreground selection, respectively. In background selection, at each stage of backcrossing, 47 parental polymorphic SSR markers were used. The graphical genotyping of the five two-gene (Xca1boXca1boPpa3Ppa3) homozygous BC2F2 plants showed an average recovery of 85.44% of the Pusa Meghna genome with highest genome recovery of 91.7%. The genome contribution of donor parents (BR-161 and BR-2) was 8.26 with 6.34% of residual heterozygousity. The backcross derived pyramided lines BC2F2:3-7-16 and BC2F2:3-7-33 showed high resistance to both the diseases and exhibited higher yield and vitamin C content as compared with recipient parent Pusa Meghna. It is, therefore, evident from this study that resistant genes can be introgressed successfully into a Pusa Meghna cultivar without any yield penalty, benefitting farmers with reduced input cost and consumers with chemical residue free produce. Besides, the pyramided lines carrying dominant resistant genes can be exploited in a hybridization programme to develop hybrid(s) in cauliflower.

Marker-Assisted Backcross Breeding for Improvement of Submergence Tolerance and Grain Yield in the Popular Rice Variety ‘Maudamani’

Submergence stress due to flash floods reduces rice yield drastically in sensitive varieties. Maudamani is a high yielding popular rice variety but is highly susceptible to submergence stress. The selection of progenies carrying Sub1 and GW5 (wide-grain) enhanced the submergence stress tolerance and grain yield of theMaudamani variety by following the marker-assisted backcross breeding method. Foreground screening detected 14 BC1F1, 17 BC2F1, and 12 BC3F1 backcross progenies that carried the target QTLs for submergence tolerance and grain width. Background screening was performed in the progenies carrying the target QTL and enhanced the recovery of a recipient parent’s genome by upto 96.875% in the BC3 pyramided line. The BC3F1 plant containing the highest recipient parent genome content and the target QTLs was self-pollinated. In BC3F2 generation, the target QTLs the Sub1 and GW5 (wide-grain) alleles and recipient parent’s yield component QTL OsSPL14 were tracked for homozygous states in the progenies. Seven pyramided lines showed tolerance to submergence for 14 days and higher grain yield than both the parents. The pyramided lines were similar to the recipient parent for the majority of the studied morphological and quality traits. The pyramided lines are useful as cultivars and can serve as potential donors for transfer of Sub1, OsSPL14, Gn1a, GW5 (wide-grain), and SCM2 QTLs.

Marker-Assisted Introgression and Stacking of Major QTLs Controlling Grain Number (Gn1a) and Number of Primary Branching (WFP) to NERICA Cultivars

The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of them were cloned, only a few were utilized for actual systematic introgression breeding programs. In this study, the major yield QTLs Grain Number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP) were introgressed and stacked in selected NERICA cultivars by marker-assisted backcross breeding (MABB). The DNA markers RM3360, RM3452, and RM5493 were used for foreground selection. At BC3F4 and BC3F5 generation, a combination of marker-assisted selection and phenotypic evaluation were carried out to select lines with target alleles and traits. Further, genotyping-by-sequencing (GBS) was conducted to validate the introgression and determine the recurrent parent genome recovery (RPGR) of the selected lines. The Gn1a and/or WFP introgression lines showed significantly higher numbers of spikelets per panicle and primary branching compared to the recurrent parents. In addition, lines with Gn1a and/or WFP alleles were comparatively similar to the recurrent parents (RP) in most yield-related traits. This study demonstrates the success of utilizing yield QTLs and marker-assisted selection to develop and improve rice cultivars.

Development of white-grain pre-harvest sprouting tolerant and pyramided protein-rich leaf rust resistant wheats using molecular breeding

The present study was undertaken for developing pre-harvest sprouting tolerant (PHST) wheat genotypes using marker-assisted backcross breeding (MABB). A major QTL for PHST was introgressed into an elite Indian wheat cv. Lok1 that is PHS susceptible. These PHST lines were also pyramided with one gene each for high grain protein content (Gpc-B1) and leaf rust resistance (Lr24). For introgression of PHST QTL, initially Lok1 was separately crossed with each of the two donors (PHS tolerant white-grained AUS1408 and CN19055). Backcrossing in each generation was followed by foreground and background selections using SSR markers. In advanced lines, KASP assay was also carried out for the candidate gene TaMKK3-A underlying the PHST QTL. The MAS derived lines homozygous for PHST QTL were screened for PHS using simulated rain chambers resulting in the selection of 10 PHST lines. For pyramiding of three QTL/genes (PHST QTL, Gpc-B1, and Lr24), MABB derived BC4F2 plants (from the cross Lok1/CN19055) were crossed with a MAS derived BC2F5 line [Lok1 (Gpc-B1 + Lr24)] developed earlier by us in the same background of Lok1. After foreground MAS followed by PHS screening, four advanced lines carrying all the three QTL/genes in homozygous condition were selected. These lines exhibited high level of PHST (PHS score 2–3) associated with significant improvement in GPC with no yield penalty and resistance against leaf rust under artificial epiphytotic conditions.