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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.

Hot pepper (Capsicum annuum var. annuum) and bell pepper (C. annuum var. grossum) are the important crops of the Solanaceae family. In the present study, marker-assisted selection (MAS) was employed for interspecific leaf curl virus disease (LCVD) resistant gene introgression from hot pepper (S-343) to heat-tolerant bell pepper lines. Segregating populations were developed using resistant (S-343) and susceptible (bell pepper) genotypes for understanding the genetics of LCVD resistance. The micro-cage artificial screening technique was used for the phenotypic selection of LCVD resistant plants from progenies of each population. The F1 of all crosses were resistant to LCVD, while F2­ and BC1F2­ generations of all the crosses were segregated into 3:1 (resistant: susceptible) and BC1F1 generations of all crosses were a good fit to ratio 1:1 (resistant:susceptible) suggesting monogenic dominant control of LCVD resistance. In addition to phenotypic selection for LCVD resistance, MAS for non-pungency was done using ‘BF7’ and ‘BR9’-SCAR primers along with the very stringent phenotyping (background selection) in backcrossed populations for most important fruit traits. The background selection was performed for the recovery of recurrent parent phenome (RPP) and it was measured as shift in means of these important fruit traits. To the best of our knowledge, it is a novel experiment of introgression of LCVD resistance in heat tolerant bell pepper lines that led to the successful development of six improved LCVD resistant, heat-tolerant and non-pungent BC2F1 populations (LCVRS3SM-1, LCVRS3SM-2, LCVRS3SM-8, LCVRS3SM-4, LCVRS3SM-17, and LCVRS3SM-58) that will help in future bell pepper resistant breeding programs.

Background Rice is a high silicon-accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crop plants. However, presence of high silica content is detrimental in rice straw and its management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in North-Western India and it is eventually burned in situ by the farmers contributing to air pollution. A practical solution to the said issue could lie in reducing the silica content in rice, while also attaining sound plant growth. Results A set of 258 Oryza nivara accessions along with 25 cultivated varieties were used to assess the variation for straw silica content using molybdenum blue colorimetry method. Large and continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08-16%, while it varied from 7.95–15.81% in the cultivated varieties. The O. nivara accessions containing 43–54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphism (SNP) among the 258 O. nivara accessions were used for estimating population structure and genome wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported QTLs. Twelve out of the 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses among the QTL regions revealed the presence of promising candidate genes, including ABC transporter, Casparian thickening genes, multi-drug and toxin extrusion (MATE) protein, F-box domains, and MYB-transcription factor domains. Besides ortho-QTLs among rice and maize genomes were also identified which could open up ways for further genetic analysis of this trait. Conclusion The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programmes in order to develop rice varieties with lower silica content along with higher yield potential.

Genetic improvement of seed yield per plant (SY) is one of the major objectives in Brassica napus breeding programme. SY, being a complex quantitative trait is directly and indirectly influenced by yield-component traits such as siliqua length (SL), number of seeds per siliqua (NSS), and thousand seed weight (TSW). Therefore, concurrent improvement in SL, NSS and TSW can lead to higher SY in B. napus. This study was conducted to identify significant SNPs and putative candidate genes governing SY and its component traits (SL, NSS, TSW). All these traits were evaluated in a diverse set of 200 genotypes representing diversity from wide geographical locations. Of these, a set of 125 genotypes were chosen based on pedigree diversity and multi-location trait variation for genotyping by sequencing (GBS). Best linear unbiased predictors (BLUPs) of all the traits were used for genome-wide association study (GWAS) with 85,126 SNPs obtained from GBS. A total of 16, 18, 27 and 18 SNPs were found to be significantly associated for SL, NSS, TSW and SY respectively. Based on linkage disequilibrium decay analysis, 150 kb genomic region flanking the SNP was used for the identification of underlying candidate genes for each test trait. Important candidate genes involved in phytohormone signaling (WAT1, OSR1, ARR8, CKX1, REM7, REM9, BG1) and seed storage proteins (Cruciferin) were found to have significant influence on seed weight and yield. Genes involved in sexual reproduction and fertilization (PERK7, PERK13, PRK3, GATA15, NFD6) were found to determine the number of seeds per siliqua. Several genes found in this study namely ATS3A, CKX1, SPL2, SPL6, SPL9, WAT1 showed pleiotropic effect with yield component traits. Significant SNPs and putative candidate genes identified for SL, NSS, TSW and SY could be used in marker-assisted breeding for improvement of crop yield in B. napus. Genotypes identified with high SL, NSS, TSW and SY could serve as donors in crop improvement programs in B. napus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01060-9.

Ascochyta blight (AB) and botrytis grey mould (BGM) are the most devastating fungal diseases of chickpea worldwide. The wild relative of chickpea, C. reticulatum acc. ILWC 292 was found resistant to BGM whereas, GPF2 (Cicer arietinum L.) is resistant to AB. A total of 187 F8 Recombinant Inbred Lines (RILs) developed from an inter-specific cross of GPF2 × C. reticulatum acc. ILWC 292 were used to identify quantitative trait loci (QTLs) responsible for resistance to AB and BGM. RILs along with parents were evaluated under artificial epiphytotic field/laboratory conditions for two years. Highly significant differences (P < 0.001) were observed for reaction to both pathogens in both years. Parents and RILs were genotyped-by-sequencing to identify genome wide single nucleotide polymorphism (SNPs). A total of 1365 filtered and parental polymorphic SNPs were used for linkage map construction, of which, 673 SNPs were arranged on eight linkage groups. Composite interval mapping revealed three QTLs for AB and four QTLs for BGM resistance. Out of which, two QTLs for AB and three QTLs for BGM were consistent in both years. These QTLs can be targeted for further fine mapping for deployment of resistance to AB and BGM in elite chickpea cultivars using marker-assisted-selection.

Cotton leaf curl disease (CLCuD), caused by a geminivirus complex, is the most serious disease of upland cotton in northwest India and Pakistan. It results in substantial losses in cotton yield and fibre quality. Due to continuous appearance of new viral strains, all the established CLCuD resistant stocks, extant and obsolete cultivars of upland cotton have become susceptible. Therefore, it became crucial to explore the novel sources of CLCuD resistance, as development of CLCuD resistant varieties is the most practical approach to manage this menace. Here, for the first time, we report introgression and mapping of CLCuD resistance from a 'synthetic cotton polyploid' to upland cotton. A backcross population (synthetic polyploid /

False smut of rice caused by Ustilaginoidea virens (Cooke) Takahashi (teleomorph Villosiclava virens) has emerged as a serious concern in rice production. While variation for resistance exists in rice germplasm, most of the cultivated varieties are susceptible to false smut. A total of 125 diverse lines from global rice diversity panel were screened for resistance to false smut along with susceptible checks GSR123 and PR116, under natural hot spot for 3 years at two different locations and artificial inoculation conditions in a fourth consecutive year. False smut resistance was recorded based on infected panicles per plants (IPP), number of smut balls per plant (NSBP) and a disease score (DS). Of 125, 21 germplasm lines showed high level of resistance in all the years under natural hot spot as well as artificial inoculation conditions whereas 31 germplasm lines showed moderate resistance. Genome wide association study for false smut related traits identified significant associations on chromosomes 2, 3, 6, 9 and 11 for IPP. Similarly, significant associations for NSBP were identified on chromosomes 3 and 8 and DS on chromosomes 3, 4 and 11. Most of these QTLs were found to be associated with all the traits. The study highlights the potential donors for resistance to false smut that could be utilized in rice breeding programme. The identified QTLs could be the potential candidate regions for further studying the false smut resistance.

Wheat breeders frequently evaluate large numbers of germplasm and segregating populations for selection in field trials. For testing large number of germplasms under complete block design not much suitable because their assumption to accommodate all the treatment combination in each block that increase the size of experiment and reduce the accuracy. To avoid this constraint the present experiment was designed with objective to realise the suitability of alpha lattice design (ALD) over randomised complete block design (RCBD) in plant breeding experiments. The present experiment was conducted in ALD of 8 × 20 i.e. eight blocks each with 20 genotypes in two replications under rainfed and restricted irrigated conditions to estimate the drought tolerance indices. Nine drought tolerance indices were estimated using the data of rainfed and restricted irrigated conditions. These drought tolerance indices were subjected to analysis of variances of both the designs ALD and RCBD to know the efficiency of ALD over RCBD. The relative efficiency of trials shows that ALD was more efficient than RCB design. Based on grain yield per plant under both the conditions twenty-one tolerant genotypes and eleven susceptible genotypes were identified. Identified tolerant and susceptible genotypes can be used for development of mapping populations and for QTLs mapping programme for drought tolerance in wheat (Triticum aestivum L.).

Wild relatives of rice (Oryza sativa L.) represent enormous genetic diversity for many traits. Many domestication related traits found only in wild species that are lost from cultivated species during domestication. In this study, we report high-resolution mapping of two domestications related quantitative trait locus (QTL) controlling purple sheath color and plant height using high-density SNP based linkage map in an interspecific F2 population derived from a cross between O. nivara Sharma & Shastry and O. sativa. The segregation ratio of purple sheath color fit into 3:1 indicated that the presence of a dominant gene. The segregation of plant height trait exhibited a normal distribution in F2 and F2:3 generations. QTL analysis showed the identification of two QTLs controlling purple sheath color (designated as qPsh6.1 and qPsh6.2) on chromosome 6 explaining 27.12% and 14% phenotypic variance, respectively. The only plant height QTL (tentatively designated as qPh1.9) was mapped on chromosome 1 contributing 18.3% phenotypic variance. The qPsh6.1 covers 25.17 Kb region flanked by AX-95928721 and AX-95954573 containing five open reading frames (ORFs) while qPsh6.2 spanned in 118.2 Kb region containing 19 ORFs flanked by markers AX-95956260 and AX-95928295. The qPh1.9 gene controlling plant height was mapped between two SNP markers, AX-95944819 and AX-95964796 co-segregated with the locus LOC_Os01g66690 encoding for ZIP4/SPO22 protein. The detailed genetic study of the location of these genes will be useful for the map-based cloning.

A novel recessive bacterial blight resistance locus designated as a xa-45(t) was identified from Oryza glaberrima accession IRGC 102600B, transferred to O. sativa and mapped to the long arm of chromosome 8 using ddRAD sequencing approach. The identified QTL spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. An STS marker developed from the locus LOC_Os08g42410 was found co-segregating with the trait and will be useful for marker-assisted transfer of this recessive resistance gene in breeding programs. Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is one of the major constraints of rice productivity in Southeast Asia. In spite of having 44 bacterial blight resistance genes from cultivated rice and wild species, the durability of resistance is always at stake due to the continually evolving nature of the pathogen and lack of suitable chemical control. Here, we report high-resolution genetic mapping of a novel bacterial blight resistance gene tentatively designated as a xa-45(t) from an introgression line derived from Oryza glaberrima accession IRGC 102600B. This introgression line was crossed with the susceptible rice indica cultivar cv. Pusa 44 to generate F2 and F2:3 populations for inheritance and mapping studies. The inheritance studies revealed the presence of single recessive locus controlling resistance to the Xanthomonas pathotype seven. A high-density linkage map was constructed using double-digest restriction-associated DNA sequencing of 96 F2 populations along with the parents. The QTL mapping identified a major locus on the long arm of rice chromosome 8 with a LOD score of 33.22 between the SNP markers C8.26737175 and C8.26818765. The peak marker, C8.26810477, explains 49.8% of the total phenotypic variance and was positioned at 202.90 cM on the linkage map. This major locus spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. A co-segregating STS marker was developed from the LOC_Os08g42410 for efficient transfer of this novel gene to elite cultivars.

Drought is a major abiotic stress that drastically reduces chickpea yields. The present study was aimed to identify drought-responsive traits in chickpea by screening a recombinant inbred line population derived from an inter-specific cross between drought cultivar of GPF2 (C. arietinum L.) and drought sensitive accession of ILWC292 (C. reticulatum), at two locations in India. Twenty-one traits, including twelve morphological and physiological traits and nine root-related traits were measured under rainfed (drought-stress) and irrigated conditions (no-stress). High genotypic variation was observed among RILs for yield and root traits indicated that selection in these germplasms would be useful in achieving genetic progress. Both correlation and principal component analysis revealed that plant height, number of pods per plant, biomass, 100-seed weight, harvest index, membrane permeability index, and relative leaf water content were significantly correlated with yield under both irrigated and drought stress environments. Root length had significant positive correlations with all root-related traits except root length density in drought-stressed plants. Path analysis and multiple and stepwise regression analyses showed that number of pods per plant, biomass, and harvest index were major contributors to yield under drought stress conditions. Thus, a holistic approach across these analyses identified number of pods per plant, biomass, harvest index, and root length as key traits for improving chickpea yield through indirect selection for developing drought-tolerant cultivars. Overall, on the basis of yield components morphological and root traits, a total of 15 promising RILs were identified for their use in chickpea breeding programs for developing drought tolerant cultivars. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-022-01218-z.

Salinized hydroponic culture experiment with three salinity levels (EC control, 6 and 12 dS/m) was performed to screen salt tolerant mutants of aerobic rice cultivar Nagina 22 and to study the nature of salt tolerance from a total of 432 EMS induced M4 mutants. Plants were harvested 30 days after sowing. Growth parameters viz. root weight, shoot weight, root length, shoot length, Na and K concentrations in shoot and roots were measured. Combined Factor scores of growth parameters was computed by Principle Component Analysis using Minitab software.At EC 12 dS/m 10 mutants out of 432 were able to survive. At moderate salinity, some mutant lines produced higher shoot weight compared to their respective control showing inverse trend and the effectiveness of EMS induced mutation in inducing salinity tolerance to these mutants. At high salinity only10 mutants survived (remained green) up to the time of 30 days harvest. These mutants performed well in terms of overall growth recording 2.1-2.5 times higher factor score and 8-14 times higher shoot weight compared to the N 22 check. One mutant N22-L-1010 almost completely excluded Na at xylem parenchyma level. Two other mutants N22-L-1013 and N22-L-806 maintained Na exclusion compared to the N22 check. N22 check and mutant N22-L-1009 maintained similar degree of Na exclusion though the N22 check died because it cannot maintain adequate K in shoot.We conclude that EMS has induced salinity tolerance in some mutants. The study can be advanced further to characterize the putative mutants through molecular genetics approaches.

The gene-for-gene relationship of host-pathogen interaction explained by H. H. Flor in mid of the 20th century set a milestone in understanding the biochemical and genetic basis of plant diseases and several components involved in plant-pathogen interactions. It highlighted the importance of accomplishing differential sets and understanding the pathogen population structure, it further led to the identification and cloning of several resistance (

The gene-for-gene relationship of host-pathogen interaction explained by H. H. Flor in mid of the 20th century set a milestone in understanding the biochemical and genetic basis of plant diseases and several components involved in plant-pathogen interactions. It highlighted the importance of accomplishing differential sets and understanding the pathogen population structure, it further led to the identification and cloning of several resistance (R) genes in plants. These R genes have been deployed and altered for fighting against diseases in a large number of crops using various conventional approaches and biotechnological tools. Identification of R genes and their corresponding Avr genes in many cases played a significant role in understanding of R-Avr gene interactions. Rapid cloning of R genes and editing of susceptible R genes are the other avenues that have broadened the horizon of utilizing R genes in crop improvement programmes. Further, combining R genes with quantitative disease resistance genes has paved the way to develop durable resistance in cultivars. The recent advances in genetics, genomics, bioinformatics and other OMICS tools are now providing greater prospects for deeper understanding of host-pathogen interaction.

Breeding for insect resistant varieties has been central to the integrated pest management as it offers an ecologically viable approach agianst biotic constraints. Considerable progress has been made in the past to incorporate resistance to insect pests of rice using conventional breeding approaches. However the diversity in insect pest population, continuous selection of virulent biotypes, lack of resistance sources in cultivated rice (Oryza sativa and O. glaberrima) gene pool, want of efficient insect rearing and varietal screening protocols and inherently complex genetics of resistance further necessitates supplementation of conventional breeding techniques with advanced molecular approaches. Hence, alternative approaches like wide hybridization to introgress resistance from other species of Oryza, transgenic approach to deploy Bt cry, snowdrop lectin and other plant derived genes are being actively pursued. The increasingly identified, mapped, cloned and characterized quantitative trait loci and genes related to insect resistance traits in rice have provided a solid foundation for direct selection and varietal improvement through molecular breeding. Utilization of DNA-based markers provided additional impetus to efficiency and precision of conventional plant breeding via marker-assisted selection to successfully introgress several genes for resistance to insect pests of rice. RNA interference technology has offered another reliable tool in meeting the challenges imposed by crop insects by targeting the enzymes/proteins integral to various biological processes of crop insects. This review briefly discusses the current progress and future prospects in molecular breeding for enhanced varietal tolerance to insect pests of rice.

Increasing seed oil content (SOC) is one of the important breeding objectives in canola quality Brassica napus, a second largest oil producing oilseed crop after soybean in the world. A fixed diversity stock of 200 canola quality genotypes, acquired from diverse geographical locations, was evaluated for SOC across environments. An association mapping panel was constituted and genotyped using genotype-by-sequencing. Significant variation was observed for genotypes, environment and genotype-by environment interaction in SOC. Best linear unbiased predictors (BLUPs) was used for genome-wide association study (GWAS) with 85,126 SNPs. A total of 14 SNPs on four chromosomes i.e., A03, A07, A09 and C05 was found significantly associated with SOC. Four SNPs (three on A07, one on A09) were significantly associated with SOC across the environments. Genomic region identified on chromosome A09 was previously reported to be associated with oleic acid content, a major component of SOC in B. napus. Novel SNPs associated with SOC were identified on chromosomes A03, A07 and C05. Candidate genes involved in regulation of lipid metabolism and biosynthesis were identified within confidence interval of SOC associated SNPs. It suggests complex mechanism due to the role of multiple direct and indirect genes governing the SOC in B. napus. A set of 15 genotypes having high oil content across the years and locations, were recommended for commercial breeding targeted to SOC improvement. This study provides insight for further improvement of SOC in B. napus through molecular breeding and marker assisted selection.

This study was designed to identify the drought tolerant and susceptible genotypes among 160 wheat genotypes. Analysis of variance under drought condition showed mean square due to genotypes had highly significant differences for all the quantitative traits in both years and pooled data, except flag leaf width, flag leaf area those were significant only and under control condition. Mean square due to genotypes had highly significant differences for all the traits in both the years and pooled data, except plant height in the pooled data that was significant only. On the basis of grain yield per plant under both the conditions twenty one tolerant genotypes namely; DBW 39, FLW 13, FLW 7, HD 2833, HD 3093, HI 1500, HI 617, HW 2004, HW 2005, HW 2066, HW 4002, HW 4008, HW 4029, HW 4215, Lok 1, Lok 65, MACS 2496, RAJ 4037, SOKOLL, SSRT 14, VJ 99 were selected and eleven susceptible genotypes using same criteria namely; DBW 14, DBW 28, DBW 88, HD 2824, HD 2877, NW 1014, PBW 343, PBW 373, RAJ 4083, UP 2828, MACS 6272 were identified. Identified tolerant and susceptible genotypes can be used for development of mapping populations to map the QTLs for drought tolerance in wheat (Triticum aestivum L.). Doi.org/10.25174/2582-2675/2020/96419

Ascochyta blight (AB) and botrytis grey mould (BGM) are the most devastating fungal diseases of chickpea worldwide. The wild relative of chickpea, C. reticulatum acc. ILWC 292 was found resistant to BGM whereas, GPF2 (Cicer arietinum L.) is resistant to AB. A total of 187 F8 Recombinant Inbred Lines (RILs) developed from an inter-specific cross of GPF2 × C. reticulatum acc. ILWC 292 were used to identify quantitative trait loci (QTLs) responsible for resistance to AB and BGM. RILs along with parents were evaluated under artificial epiphytotic field/laboratory conditions for two years. Highly significant differences (P < 0.001) were observed for reaction to both pathogens in both years. Parents and RILs were genotyped-by-sequencing to identify genome wide single nucleotide polymorphism (SNPs). A total of 1365 filtered and parental polymorphic SNPs were used for linkage map construction, of which, 673 SNPs were arranged on eight linkage groups. Composite interval mapping revealed three QTLs for AB and four QTLs for BGM resistance. Out of which, two QTLs for AB and three QTLs for BGM were consistent in both years. These QTLs can be targeted for further fine mapping for deployment of resistance to AB and BGM in elite chickpea cultivars using marker-assisted-selection.

Plant breeding is the science that deals with improving the genetic architecture of crop plants for benefit of human beings. Increasing food demand with rising world population, changing food habits and changing climate adversely affecting the plant growth requires accelerating plant breeding activities. Most of the traits in the different growth phases of a plant are quantitative and complex in nature. These traits show continuous distribution of phenotypes in segregating populations and are controlled by number of genes, environment and their interaction. The branch of quantitative genetics aims to understand and manipulate these traits for improving the crop plants. The classical methods to study quantitative traits include the partitioning of total phenotypic variation into environmental and different components of genetic variation. It was also possible to predict the number of genes controlling a quantitative trait in the form of “K-factors” and “effective factors”. Though these methods helped to decide appropriate plant breeding strategy and response to selection, the number, location and specific action of factors (genes) controlling quantitative traits remained obscure. With the advent of molecular markers, new avenues opened up to determine the location of such genes in the form of quantitative trait loci (QTL) by developing different kinds of mapping populations. However mapping and cloning of QTL was still an arduous task due to time involved in development of mapping populations and utilization of molecular markers in scanning the whole genome. The advancements in the field of sequencing, high-throughput genotyping and phenotyping accelerated the mapping and cloning of QTL and their utilization in plant breeding programme through marker-assisted and/or genomic selection. This chapter will discuss the various strategies that advanced the science of quantitative genetics in the past one and half decade and its role in accelerating crop improvement programmes.

A BPH-resistant locus designated as Bph34 identified in Oryza nivara acc. IRGC104646 on long arm of chromosome 4 using high-resolution mapping with 50 K SNP chip. BPH resistance contributed by locus showed dominant inheritance in F2 and F3. The Bph34 locus is 91 kb in size and contains 11 candidate genes. In addition to SNP markers, SSR markers, RM16994 and RM17007 co-segregated with the BPH resistance. These two SSR markers can facilitate marker-assisted transfer of the Bph34 locus into elite rice cultivars in all labs. Brown planthopper (BPH, Nilaparvata lugen Stal) is one of the most destructive insects of rice (Oryza sativa L.) causing significant yield losses annually. Exploiting host plant resistance to BPH and incorporating resistant genes in susceptible commercial cultivars is economical and environmentally friendly approach to manage this pest. Here, we report high-resolution mapping of a novel genetic locus for resistance to BPH, designated as Bph34 on long arm of rice chromosome 4. The locus was mapped using an interspecific F2 population derived from a cross between susceptible indica cultivar PR122 and BPH-resistant wild species, O. nivara acc. IRGC104646. Inheritance studies performed using F2 and F2:3 populations revealed the presence of single dominant gene. Construction of high-density linkage map using 50 K SNP chip (OsSNPnks) followed by QTL mapping identified single major locus at 28.8 LOD score between SNP markers, AX-95952039 and AX-95921548. The major locus contributing resistance to BPH designated as Bph34 and explained 68.3% of total phenotypic variance. The Bph34 locus is 91 Kb in size on Nipponbare reference genome-IRGSP-1.0 and contains 11 candidate genes. In addition to associated SNP markers, two SSR markers, RM16994 and RM17007, also co-segregated with the Bph34 which can be used efficiently for markers assisted transfer into elite rice cultivars across the labs.

Heat stress during reproductive stages has been leading to significant yield losses in chickpea (Cicer arietinum L.). With an aim of identifying the genomic regions or QTLs responsible for heat tolerance, 187 F8 recombinant inbred lines (RILs) derived from the cross GPF 2 (heat tolerant) × ILWC 292 (heat sensitive) were evaluated under late-sown irrigated (January-May) and timely-sown irrigated environments (November-April) at Ludhiana and Faridkot in Punjab, India for 13 heat tolerance related traits. The pooled ANOVA for both locations for the traits namely days to germination (DG), days to flowering initiation (DFI), days to 50% flowering (DFF), days to 100% flowering (DHF), plant height (PH), pods per plant (NPP), biomass (BIO), grain yield (YLD), 100-seed weight (HSW), harvest index (HI), membrane permeability index (MPI), relative leaf water content (RLWC) and pollen viability (PV)) showed a highly significant difference in RILs. The phenotyping data coupled with the genetic map comprising of 1365 ddRAD-Seq based SNP markers were used for identifying the QTLs for heat tolerance. Composite interval mapping provided a total of 28 and 23 QTLs, respectively at Ludhiana and Faridkot locations. Of these, 13 consensus QTLs for DG, DFI, DFF, DHF, PH, YLD, and MPI have been identified at both locations. Four QTL clusters containing QTLs for multiple traits were identified on the same genomic region at both locations. Stable QTLs for days to flowering can be one of the major factors for providing heat tolerance as early flowering has an advantage of more seed setting due to a comparatively longer reproductive period. Identified QTLs can be used in genomics-assisted breeding to develop heat stress-tolerant high yielding chickpea cultivars.

Considering the potentials of wild rice (Oryza spp.), as well as the need to enhance the yield potential of rice and to increase rice production to meet increasing demands, 1780 backcross inbred lines (BILs) were generated by crossing 70 accessions of six “AA” genome species: Oryza glaberrima Steud., Oryza barthii A. Chev., Oryza nivara Sharma & Shastry, Oryza rufipogon Griff., Oryza longistaminata A. Chev. & Roehr., and Oryza glumaepatula Steud. with two elite cultivars of Oryza sativa L. The wild species accessions were selected based on variation at the DNA markers and agromorphological traits. The BILs were generated by backcrossing F₁s twice (thrice in some cases) to recipient parents, followed by continuous selfing and selection for the yield and yield component traits. The set of 1780 BC₂F₅ to BC₂F₁₀ BILs were evaluated in an augmented design over 3 yr. Based on ANOVA in augmented design, 108 agronomically superior BILs were selected and evaluated in randomized complete block design. Of the 108 BILs evaluated, 15 BILs showed >10% yield superiority over the recurrent parent, with spikelet per panicle and thousand-grain weight as most significant traits contributing to yield increase. Based on the contribution of donor accessions for the improvement of yield component traits, six accessions of O. glaberrima, one of O. barthii, two of O. nivara, two of O. rufipogon, and one each of O. longistaminata and O. glumaepatula were identified as potential donors that could be used more rigorously in transferring genes to cultivated rice. The BILs generated in the present study represents a reservoir of novel genetic variation.

Breeding for terminal heat stress (THS) in Brassica juncea L. Czern & Coss is recognized as an imperative objective for sustained productivity in contemporary climatic changes. A fixed diversity stock of 491 genotypes was documented for wide range of variations for seed yield under natural terminal heat stress. A set of top 20 genotypes comprising introgression lines from wild species Erucastrum cardaminoides and B. tournefortii; derived B. juncea lines using B. carinata and B. napus; land races;, commercial cultivars and breeding lines, having the lowest heat susceptibility index and the least yield reduction under heat stress, have been identified as potential heat tolerant donors. A panel of 96 genotypes was constituted from this stock on the basis of their differential response to heat susceptibility index and seed yield reduction under natural THS. The constituted panel was evaluated for validation under controlled conditions for ten seed yield-related traits. Moderate to low correlations between SY and its related traits were observed in NS and THS conditions. Double digest restriction site associated DNA sequencing of 71 genotypes identified 18,258 SNPs after filtration. Least square means of all the traits under NS and THS conditions and the best linear unbiased predictors along with identified SNPs were used for genome-wide association study. A total of 34 SNPs under NS, 24SNPs under THS and 30SNPs using BLUP values were found to be associated with all seed yield-related traits. Chromosome B05 harbored the maximum number of SNPs (nine) followed by chromosomes A07 and A09 (eight SNPs each). SNPs under NS conditions could not be associated with THS. This is the first report on the identification of 24 marker-traits associations detected for SY and its component traits under THS conditions. It may be possible to develop the molecular markers for significant SNPs after due validation. The constituted panel may also serve as a source of allelic diversity for genes controlling various economic traits. The derived introgression lines as potential heat tolerant donors indicated the possibility of using wild species to breed for abiotic stress tolerance in Indian mustard.

A novel recessive bacterial blight resistance locus designated as a xa-45(t) was identified from Oryza glaberrima accession IRGC 102600B, transferred to O. sativa and mapped to the long arm of chromosome 8 using ddRAD sequencing approach. The identified QTL spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. An STS marker developed from the locus LOC_Os08g42410 was found co-segregating with the trait and will be useful for marker-assisted transfer of this recessive resistance gene in breeding programs. Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is one of the major constraints of rice productivity in Southeast Asia. In spite of having 44 bacterial blight resistance genes from cultivated rice and wild species, the durability of resistance is always at stake due to the continually evolving nature of the pathogen and lack of suitable chemical control. Here, we report high-resolution genetic mapping of a novel bacterial blight resistance gene tentatively designated as a xa-45(t) from an introgression line derived from Oryza glaberrima accession IRGC 102600B. This introgression line was crossed with the susceptible rice indica cultivar cv. Pusa 44 to generate F

Increasing the rice productivity from the current 10 to 12 tons/ha to meet the demand of estimated 8.8 billion people in 2035 is posing a major challenge. Wild relatives of rice contain some novel genes which can help in improving rice yield. Spikelet per panicle (SPP) is a valuable trait for determining yield potential in rice. In this study, a major QTL for increasing SPP has been identified, mapped, and transferred from African wild rice O. longistaminata to O. sativa (L.). The QTL was mapped on the long arm of chromosome 2 in a 167.1 kb region flanked by SSR markers RM13743 and RM13750, which are 1.0 cM apart, and is designated as qSPP2.2. The QTL explained up to 30% of phenotypic variance in different generations/seasons and showed positive additive effect of allele contributed by O. longistaminata. In addition, O. longistaminata allele in qSPP2.2 contributed to increase in grains per panicle, but decrease in the tillers per plant. The 167.1 kb region contains 23 predicted genes. Based on the functional annotation, three genes, LOC_Os02g44860, LOC_Os02g44990, and LOC_Os02g45010, were selected as putative candidates for characterization. Sequence analysis of the three genes revealed functional variations between the parental lines for LOC_Os02g44990 and a variation in 5′UTR for LOC_Os02g45010 which will help further to identify putative candidate gene(s). This is the first yield component QTL to be identified, mapped, and transferred from O. longistaminata.

A BPH-resistant locus designated as Bph34 identified in Oryza nivara acc. IRGC104646 on long arm of chromosome 4 using high-resolution mapping with 50 K SNP chip. BPH resistance contributed by locus showed dominant inheritance in F

Rice productivity is hampered by a number of diseases and insects. Among the insects, hoppers including planthoppers and leafhoppers are typical phloem-sap feeders, which are very serious and damaging insect pests of rice in Asia. Many chemicals have been recommended for the control of planthoppers, but due to their feeding habit at the base of the plant, the farmers are unable to notice and effectively control these pests. Exploiting host plant resistance to hoppers and incorporating resistant genes in commercial cultivars are an alternative, economical and environment-friendly approach. To date, approximately 70 resistance genes against hoppers have been identified, and most of these genes have been tagged with molecular markers. Recently six genes for resistance to brown planthopper (BPH) in different lines have been cloned using map-based cloning. Based on molecular analysis of cloned genes, it appears that there is considerable similarity in the plant response to BPH infestation and fungal/bacterial pathogen attack. Marker-assisted selection (MAS) and pyramiding of genes for resistance to BPH and green rice leafhopper (GRH) have shown higher level and wide spectrum of resistance than their monogenic lines. In addition, transgenic approaches including RNAi have targeted various plant lectins and volatile compounds to generate resistance to hoppers. In context of changing climate, the major challenge for plant breeders is to breed varieties while taking care of changing populations of planthoppers and biotype development. Future research priorities should concentrate on high-throughput screening of germplasm for field resistance to planthoppers, identifying and transferring new genes for resistance from different sources to broaden the gene pool of rice and identifying durable combination of genes for marker-assisted pyramiding.