High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut.

BACKGROUND: Foliar diseases namely late leaf spot (LLS) and leaf rust (LR) reduce yield and deteriorate fodder quality in groundnut. Also the high oleic acid content has emerged as one of the most important traits for industries and consumers due to its increased shelf life and health benefits. RESULTS: Genetic mapping combined with pooled sequencing approaches identified candidate resistance genes (LLSR1 and LLSR2 for LLS and LR1 for LR) for both foliar fungal diseases. The LLS-A02 locus housed LLSR1 gene for LLS resistance, while, LLS-A03 housed LLSR2 and LR1 genes for LLS and LR resistance, respectively. A total of 49 KASPs markers were developed from the genomic regions of important disease resistance genes, such as NBS-LRR, purple acid phosphatase, pentatricopeptide repeat-containing protein, and serine/threonine-protein phosphatase. Among the 49 KASP markers, 41 KASPs were validated successfully on a validation panel of contrasting germplasm and breeding lines. Of the 41 validated KASPs, 39 KASPs were designed for rust and LLS resistance, while two KASPs were developed using fatty acid desaturase (FAD) genes to control high oleic acid levels. These validated KASP markers have been extensively used by various groundnut breeding programs across the world which led to development of thousands of advanced breeding lines and few of them also released for commercial cultivation. CONCLUSION: In this study, high-throughput and cost-effective KASP assays were developed, validated and successfully deployed to improve the resistance against foliar fungal diseases and oleic acid in groundnut. So far deployment of allele-specific and KASP diagnostic markers facilitated development and release of two rust- and LLS-resistant varieties and five high-oleic acid groundnut varieties in India. These validated markers provide opportunities for routine deployment in groundnut breeding programs.

Identification and application of a candidate gene AhAftr1 for aflatoxin production resistance in peanut seed (Arachis hypogaea L.).

INTRODUCTION: Peanut is susceptible to infection of Aspergillus fungi and conducive to aflatoxin contamination, hence developing aflatoxin-resistant variety is highly meaningful. Identifying functional genes or loci conferring aflatoxin resistance and molecular diagnostic marker are crucial for peanut breeding. OBJECTIVES: This work aims to (1) identify candidate gene for aflatoxin production resistance, (2) reveal the related resistance mechanism, and (3) develop diagnostic marker for resistance breeding program. METHODS: Resistance to aflatoxin production in a recombined inbred line (RIL) population derived from a high-yielding variety Xuhua13 crossed with an aflatoxin-resistant genotype Zhonghua 6 was evaluated under artificial inoculation for three consecutive years. Both genetic linkage analysis and QTL-seq were conducted for QTL mapping. The candidate gene was further fine-mapped using a secondary segregation mapping population and validated by transgenic experiments. RNA-Seq analysis among resistant and susceptible RILs was used to reveal the resistance pathway for the candidate genes. RESULTS: The major effect QTL qAFTRA07.1 for aflatoxin production resistance was mapped to a 1.98 Mbp interval. A gene, AhAftr1 (Arachis hypogaea Aflatoxin resistance 1), was detected structure variation (SV) in leucine rich repeat (LRR) domain of its production, and involved in disease resistance response through the effector-triggered immunity (ETI) pathway. Transgenic plants with overexpression of AhAftr1(ZH6) exhibited 57.3% aflatoxin reduction compared to that of AhAftr1(XH13). A molecular diagnostic marker AFTR.Del.A07 was developed based on the SV. Thirty-six lines, with aflatoxin content decrease by over 77.67% compared to the susceptible control Zhonghua12 (ZH12), were identified from a panel of peanut germplasm accessions and breeding lines through using AFTR.Del.A07. CONCLUSION: Our findings would provide insights of aflatoxin production resistance mechanisms and laid meaningful foundation for further breeding programs.

Genetic mapping identified major main-effect and three co-localized quantitative trait loci controlling high iron and zinc content in groundnut.

Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.

Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut.

Groundnut productivity and quality have been impeded by rising temperatures in semi-arid environments. Hence, understanding the effects and molecular mechanisms of heat stress tolerance will aid in tackling yield losses. In this context, a recombinant inbred line (RIL) population was developed and phenotyped for eight seasons at three locations for agronomic, phenological, and physiological traits under heat stress. A genetic map was constructed using genotyping-by-sequencing with 478 single-nucleotide polymorphism (SNP) loci spanning a map distance of 1,961.39 cM. Quantitative trait locus (QTL) analysis using phenotypic and genotypic data identified 45 major main-effect QTLs for 21 traits. Intriguingly, three QTL clusters (Cluster-1-Ah03, Cluster-2-Ah12, and Cluster-3-Ah20) harbor more than half of the major QTLs (30/45, 66.6%) for various heat tolerant traits, explaining 10.4%-38.6%, 10.6%-44.6%, and 10.1%-49.5% of phenotypic variance, respectively. Furthermore, important candidate genes encoding DHHC-type zinc finger family protein (arahy.J0Y6Y5), peptide transporter 1 (arahy.8ZMT0C), pentatricopeptide repeat-containing protein (arahy.4A4JE9), Ulp1 protease family (arahy.X568GS), Kelch repeat F-box protein (arahy.I7X4PC), FRIGIDA-like protein (arahy.0C3V8Z), and post-illumination chlorophyll fluorescence increase (arahy.92ZGJC) were the underlying three QTL clusters. The putative functions of these genes suggested their involvement in seed development, regulating plant architecture, yield, genesis and growth of plants, flowering time regulation, and photosynthesis. Our results could provide a platform for further fine mapping, gene discovery, and developing markers for genomics-assisted breeding to develop heat-tolerant groundnut varieties.

Whole-genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut.

Seed weight in groundnut (Arachis hypogaea L.) has direct impact on yield as well as market price because of preference for bold seeds by consumers and industry, thereby making seed-size improvement as one of the most important objectives of groundnut breeding programs globally. Marker-based early generation selection can accelerate the process of breeding for developing large-seeded varieties. In this context, we deployed the quantitative trait locus-sequencing (QTL-seq) approach on a biparental mapping population (Chico × ICGV 02251) to identify candidate genes and develop markers for seed weight in groundnut. A total of 289.4-389.4 million reads sequencing data were generated from three libraries (ICGV 02251 and two extreme bulks) achieving 93.9-95.1% genome coverage and 8.34-9.29× average read depth. The analysis of sequencing data using QTL-seq pipeline identified five genomic regions (three on chromosome B06 and one each on chromosomes B08 and B09) for seed weight. Detailed analysis of above associated genomic regions detected 182 single-nucleotide polymorphisms (SNPs) in genic and intergenic regions, and 11 of these SNPs were nonsynonymous in the genomic regions of 10 candidate genes including Ulp proteases and BIG SEED locus genes. Kompetitive allele specific polymerase chain reaction (KASP) markers for 14 SNPs were developed, and four of these markers (snpAH0031, snpAH0033, snpAH0037, and snpAH0038) were successfully validated for deployment in breeding for large-seeded groundnut varieties.

Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding.

Profiling the genetic composition and relationships among groundnut germplasm collections is essential for the breeding of new cultivars. The objectives of this study were to assess the genetic diversity and population structure among 100 improved groundnut genotypes using agronomic traits and high-density single nucleotide polymorphism (SNP) markers. The genotypes were evaluated for agronomic traits and drought tolerance at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)/India across two seasons. Ninety-nine of the test genotypes were profiled with 16363 SNP markers. Pod yield per plant (PY), seed yield per plant (SY), and harvest index (HI) were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes ICGV 07222, ICGV 06040, ICGV 01260, ICGV 15083, ICGV 10143, ICGV 03042, ICGV 06039, ICGV 14001, ICGV 11380, and ICGV 13200 ranked top in terms of pod yield under both drought-stressed and optimum conditions. PY exhibited a significant (p ≤ 0.05) correlation with SY, HI, and total biomass (TBM) under both test conditions. Based on the principal component (PC) analysis, PY, SY, HSW, shelling percentage (SHP), and HI were allocated in PC 1 and contributed to the maximum variability for yield under the two water regimes. Hence, selecting these traits could be successful for screening groundnut genotypes under drought-stressed and optimum conditions. The model-based population structure analysis grouped the studied genotypes into three sub-populations. Dendrogram for phenotypic and genotypic also grouped the studied 99 genotypes into three heterogeneous clusters. Analysis of molecular variance revealed that 98% of the total genetic variation was attributed to individuals, while only 2% of the total variance was due to variation among the subspecies. The genetic distance between the Spanish bunch and Virginia bunch types ranged from 0.11 to 0.52. The genotypes ICGV 13189, ICGV 95111, ICGV 14421, and ICGV 171007 were selected for further breeding based on their wide genetic divergence. Data presented in this study will guide groundnut cultivar development emphasizing economic traits and adaptation to water-limited agro-ecologies, including in Ethiopia.

Genome-based trait prediction in multi- environment breeding trials in groundnut.

KEY MESSAGE: Comparative assessment identified naïve interaction model, and naïve and informed interaction GS models suitable for achieving higher prediction accuracy in groundnut keeping in mind the high genotype × environment interaction for complex traits. Genomic selection (GS) can be an efficient and cost-effective breeding approach which captures both small- and large-effect genetic factors and therefore promises to achieve higher genetic gains for complex traits such as yield and oil content in groundnut. A training population was constituted with 340 elite lines followed by genotyping with 58 K 'Axiom_Arachis' SNP array and phenotyping for key agronomic traits at three locations in India. Four GS models were tested using three different random cross-validation schemes (CV0, CV1 and CV2). These models are: (1) model 1 (M1 = E + L) which includes the main effects of environment (E) and line (L); (2) model 2 (M2 = E + L + G) which includes the main effects of markers (G) in addition to E and L; (3) model 3 (M3 = E + L + G + GE), a naïve interaction model; and (4) model 4 (E + L + G + LE + GE), a naïve and informed interaction model. Prediction accuracy estimated for four models indicated clear advantage of the inclusion of marker information which was reflected in better prediction accuracy achieved with models M2, M3 and M4 as compared to M1 model. High prediction accuracies (> 0.600) were observed for days to 50% flowering, days to maturity, hundred seed weight, oleic acid, rust@90 days, rust@105 days and late leaf spot@90 days, while medium prediction accuracies (0.400-0.600) were obtained for pods/plant, shelling  %, and total yield/plant. Assessment of comparative prediction accuracy for different GS models to perform selection for untested genotypes, and unobserved and unevaluated environments provided greater insights on potential application of GS breeding in groundnut.

Advances in Crop Improvement and Delivery Research for Nutritional Quality and Health Benefits of Groundnut (Arachis hypogaea L.).

Groundnut is an important global food and oil crop that underpins agriculture-dependent livelihood strategies meeting food, nutrition, and income security. Aflatoxins, pose a major challenge to increased competitiveness of groundnut limiting access to lucrative markets and affecting populations that consume it. Other drivers of low competitiveness include allergens and limited shelf life occasioned by low oleic acid profile in the oil. Thus grain off-takers such as consumers, domestic, and export markets as well as processors need solutions to increase profitability of the grain. There are some technological solutions to these challenges and this review paper highlights advances in crop improvement to enhance groundnut grain quality and nutrient profile for food, nutrition, and economic benefits. Significant advances have been made in setting the stage for marker-assisted allele pyramiding for different aflatoxin resistance mechanisms-in vitro seed colonization, pre-harvest aflatoxin contamination, and aflatoxin production-which, together with pre- and post-harvest management practices, will go a long way in mitigating the aflatoxin menace. A breakthrough in aflatoxin control is in sight with overexpression of antifungal plant defensins, and through host-induced gene silencing in the aflatoxin biosynthetic pathway. Similarly, genomic and biochemical approaches to allergen control are in good progress, with the identification of homologs of the allergen encoding genes and development of monoclonal antibody based ELISA protocol to screen for and quantify major allergens. Double mutation of the allotetraploid homeologous genes, FAD2A and FAD2B, has shown potential for achieving >75% oleic acid as demonstrated among introgression lines. Significant advances have been made in seed systems research to bridge the gap between trait discovery, deployment, and delivery through innovative partnerships and action learning.

Whole-genome resequencing-based QTL-seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut.

The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human-made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy-to-use genetic markers enables early-generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL-seq approach for identification of key genomic regions and candidate genes. Whole-genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta-SNP index and identified a total of 10,759 genomewide high-confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes-RING-H2 finger protein and zeaxanthin epoxidase-were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL-seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.

Steady expression of high oleic acid in peanut bred by marker-assisted backcrossing for fatty acid desaturase mutant alleles and its effect on seed germination along with other seedling traits.

Peanut (Arachis hypogaea L.) is an important nutrient-rich food legume and valued for its good quality cooking oil. The fatty acid content is the major determinant of the quality of the edible oil. The oils containing higher monounsaturated fatty acid are preferred for improved shelf life and potential health benefits. Therefore, a high oleic/linoleic fatty acid ratio is the target trait in an advanced breeding program. The two mutant alleles, ahFAD2A (on linkage group a09) and ahFAD2B (on linkage group b09) control fatty acid composition for higher oleic/linoleic ratio in peanut. In the present study, marker-assisted backcrossing was employed for the introgression of two FAD2 mutant alleles from SunOleic95R into the chromosome of ICGV06100, a high oil content peanut breeding line. In the marker-assisted backcrossing-introgression lines, a 97% increase in oleic acid, and a 92% reduction in linoleic acid content was observed in comparison to the recurrent parent. Besides, the oleic/linoleic ratio was increased to 25 with respect to the recurrent parent, which was only 1.2. The most significant outcome was the stable expression of oil-content, oleic acid, linoleic acid, and palmitic acid in the marker-assisted backcrossing-introgression lines over the locations. No significant difference was observed between high oleic and normal oleic in peanuts for seedling traits except germination percentage. In addition, marker-assisted backcrossing-introgression lines exhibited higher yield and resistance to foliar fungal diseases, i.e., late leaf spot and rust.

Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers.

Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP-GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large-scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega-initiatives facilitated release of a number of new varieties and also dissemination of on-the-shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics-assisted breeding approaches and rapid generation advancement.

Genetics, genomics and breeding of groundnut (Arachis hypogaea L.).

Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.

Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hypogaea L.).

Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut.

Molecular Mapping of Oil Content and Fatty Acids Using Dense Genetic Maps in Groundnut (Arachis hypogaea L.).

Enhancing seed oil content with desirable fatty acid composition is one of the most important objectives of groundnut breeding programs globally. Genomics-assisted breeding facilitates combining multiple traits faster, however, requires linked markers. In this context, we have developed two different F2 mapping populations, one for oil content (OC-population, ICGV 07368 × ICGV 06420) and another for fatty acid composition (FA-population, ICGV 06420 × SunOleic 95R). These two populations were phenotyped for respective traits and genotyped using Diversity Array Technology (DArT) and DArTseq genotyping platforms. Two genetic maps were developed with 854 (OC-population) and 1,435 (FA-population) marker loci with total map distance of 3,526 and 1,869 cM, respectively. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data identified eight QTLs for oil content including two major QTLs, qOc-A10 and qOc-A02, with 22.11 and 10.37% phenotypic variance explained (PVE), respectively. For seven different fatty acids, a total of 21 QTLs with 7.6-78.6% PVE were identified and 20 of these QTLs were of major effect. Two mutant alleles, ahFAD2B and ahFAD2A, also had 18.44 and 10.78% PVE for palmitic acid, in addition to oleic (33.8 and 17.4% PVE) and linoleic (41.0 and 19.5% PVE) acids. Furthermore, four QTL clusters harboring more than three QTLs for fatty acids were identified on the three LGs. The QTLs identified in this study could be further dissected for candidate gene discovery and development of diagnostic markers for breeding improved groundnut varieties with high oil content and desirable oil quality.

QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.).

Rust and late leaf spot (LLS) are the two major foliar fungal diseases in groundnut, and their co-occurrence leads to significant yield loss in addition to the deterioration of fodder quality. To identify candidate genomic regions controlling resistance to rust and LLS, whole-genome resequencing (WGRS)-based approach referred as 'QTL-seq' was deployed. A total of 231.67 Gb raw and 192.10 Gb of clean sequence data were generated through WGRS of resistant parent and the resistant and susceptible bulks for rust and LLS. Sequence analysis of bulks for rust and LLS with reference-guided resistant parent assembly identified 3136 single-nucleotide polymorphisms (SNPs) for rust and 66 SNPs for LLS with the read depth of ≥7 in the identified genomic region on pseudomolecule A03. Detailed analysis identified 30 nonsynonymous SNPs affecting 25 candidate genes for rust resistance, while 14 intronic and three synonymous SNPs affecting nine candidate genes for LLS resistance. Subsequently, allele-specific diagnostic markers were identified for three SNPs for rust resistance and one SNP for LLS resistance. Genotyping of one RIL population (TAG 24 × GPBD 4) with these four diagnostic markers revealed higher phenotypic variation for these two diseases. These results suggest usefulness of QTL-seq approach in precise and rapid identification of candidate genomic regions and development of diagnostic markers for breeding applications.

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens.

Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45-56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

Molecular breeding for introgression of fatty acid desaturase mutant alleles (ahFAD2A and ahFAD2B) enhances oil quality in high and low oil containing peanut genotypes.

High oleate peanuts have two marketable benefits, health benefits to consumers and extended shelf life of peanut products. Two mutant alleles present on linkage group a09 (ahFAD2A) and b09 (ahFAD2B) control composition of three major fatty acids, oleic, linoleic and palmitic acids which together determine peanut oil quality. In conventional breeding, selection for fatty acid composition is delayed to advanced generations. However by using DNA markers, breeders can reject large number of plants in early generations and therefore can optimize time and resources. Here, two approaches of molecular breeding namely marker-assisted backcrossing (MABC) and marker-assisted selection (MAS) were employed to transfer two FAD2 mutant alleles from SunOleic 95R into the genetic background of ICGV 06110, ICGV 06142 and ICGV 06420. In summary, 82 MABC and 387 MAS derived introgression lines (ILs) were developed using DNA markers with elevated oleic acid varying from 62 to 83%. Oleic acid increased by 0.5-1.1 folds, with concomitant reduction of linoleic acid by 0.4-1.0 folds and palmitic acid by 0.1-0.6 folds among ILs compared to recurrent parents. Finally, high oleate ILs, 27 with high oil (53-58%), and 28 ILs with low oil content (42-50%) were selected that may be released for cultivation upon further evaluation.

Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.).

KEY MESSAGE: Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield. Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar 'GPBD 4' into three rust susceptible varieties ('ICGV 91114', 'JL 24' and 'TAG 24') through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2-3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56-96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.

Groundnut improvement: use of genetic and genomic tools.

Groundnut (Arachis hypogaea L.), a self-pollinated legume is an important crop cultivated in 24 million ha world over for extraction of edible oil and food uses. The kernels are rich in oil (48-50%) and protein (25-28%), and are source of several vitamins, minerals, antioxidants, biologically active polyphenols, flavonoids, and isoflavones. Improved varieties of groundnut with high yield potential were developed and released for cultivation world over. The improved varieties belong to different maturity durations and possess resistance to diseases, tolerance to drought, enhanced oil content, and improved quality traits for food uses. Conventional breeding procedures along with the tools for phenotyping were largely used in groundnut improvement programs. Mutations were used to induce variability and wide hybridization was attempted to tap variability from wild species. Low genetic variability has been a bottleneck for groundnut improvement. The vast potential of wild species, reservoir of new alleles remains under-utilized. Development of linkage maps of groundnut during the last decade was followed by identification of markers and quantitative trait loci for the target traits. Consequently, the last decade has witnessed the deployment of molecular breeding approaches to complement the ongoing groundnut improvement programs in USA, China, India, and Japan. The other potential advantages of molecular breeding are the feasibility to target multiple traits for improvement and provide tools to tap new alleles from wild species. The first groundnut variety developed through marker-assisted back-crossing is a root-knot nematode-resistant variety, NemaTAM in USA. The uptake of molecular breeding approaches in groundnut improvement programs by NARS partners in India and many African countries is slow or needs to be initiated in part due to inadequate infrastructure, high genotyping costs, and human capacities. Availability of draft genome sequence for diploid (AA and BB) and tetraploid, AABB genome species of Arachis in coming years is expected to bring low-cost genotyping to the groundnut community that will facilitate use of modern genetics and breeding approaches such as genome-wide association studies for trait mapping and genomic selection for crop improvement.