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Abstract Pre-harvest sprouting (PHS) in groundnut leads to substantial yield losses and reduced seed quality, resulting in reduced market value of groundnuts. Breeding cultivars with 14–21 days of fresh seed dormancy (FSD) holds promise for precisely mitigating the yield and quality deterioration. In view of this, six multi-locus genome-wide association study (ML-GWAS) models alongside a single-locus GWAS (SL-GWAS) model were employed on a groundnut mini-core collection using multi season phenotyping and 58 K “Axiom_Arachis” array genotyping data. A total of 9 significant SNP-trait associations (STAs) for FSD were detected on A01, A04, A08, A09, B02, B04, B05, B07 and B09 chromosomes using six ML-GWAS models. Additionally, the SL-GWAS model identified 38 STAs across 14 chromosomes of groundnut. A single STA on chromosome B02 (qFSD-B02-1) was consistently identified in both ML-GWAS and SL-GWAS models. Furthermore, candidate gene mining identified nine high confidence genes viz., Cytochrome P450 705 A, Dormancy/auxin associated family protein, WRKY family transcription factor, Protein kinase superfamily protein, serine/threonine protein phosphatase, myb transcription factor, transcriptional regulator STERILE APETALA-like, ethylene-responsive transcription factor 7-like and F-box protein interaction domain protein as prime regulators involved in Abscisic acid/Gibberellic acid signaling pathways regulating dormancy/germination. In addition, three of the allele-specific markers developed from the identified STAs were validated across a diverse panel. These markers hold potential for increasing dormancy in groundnut through marker-assisted selection (MAS). Thus, this research offers insights into genetic and molecular mechanisms underlying groundnut seed dormancy in addition to providing markers and donors for breeding future varieties with 2–3 weeks of FSD.

Abstract 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.

Peanuts (Arachis hypogaea L.) with high oleic acid content have extended shelf life and several health benefits. Oleic, linoleic, and palmitic acid contents in peanuts are regulated by ahFAD2A and ahFAD2B mutant alleles. In the present study, ahFAD2A and ahFAD2B mutant alleles from SunOleic 95R were introgressed into two popular peanut cultivars, GG-7 and TKG19A, followed by markers-assisted selection (MAS) and backcrossing (MABC). A total of 22 MAS and three MABC derived lines were developed with increased oleic acid (78–80%) compared to those of GG 7 (40%) and TKG 19A (50%). Peanut kernel mineral and vitamin composition remained unchanged, while potassium content was altered in high oleic ingression lines. Two introgression lines, HOMS Nos. 37 and 113 had over 10% higher pooled pod yield than respective best check varieties. More than 70% recurrent parent genome recovery was observed in HOMS-37 and HOMS-113 through recombination breeding. However, the absence of recombination in the vicinity of the target locus resulted in its precise introgression along with ample background genome recovery. Selected introgression lines could be released for commercial cultivation based on potential pod yield and oleic acid content.

Foliar fungal diseases (rust and late leaf spot) incur large yield losses, in addition to the deterioration of fodder quality in groundnut worldwide. High oleic acid has emerged as a key market trait in groundnut, as it increases the shelf life of the produce/products in addition to providing health benefits to consumers. Marker-assisted backcrossing (MABC) is the most successful approach to introgressing or pyramiding one or more traits using trait-linked markers. We used MABC to improve three popular Indian cultivars (GJG 9, GG 20, and GJGHPS 1) for foliar disease resistance (FDR) and high oleic acid content. A total of 22 BC3F4 and 30 BC2F4 introgression lines (ILs) for FDR and 46 BC3F4 and 41 BC2F4 ILs for high oleic acid were developed. Recurrent parent genome analysis using the 58 K Axiom_Arachis array identified several lines showing upto 94% of genome recovery among second and third backcross progenies. Phenotyping of these ILs revealed FDR scores comparable to the resistant parent, GPBD 4, and ILs with high (~80%) oleic acid in addition to high genome recovery. These ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic backgrounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India. Keywords: Foliar disease resistance, High oleic acid, Late leaf spot, Marker-assisted backcrossing, SNP array, Background genome recovery

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.