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Peanut is vulnerable to a range of diseases, such as Tomato spotted wilt virus (TSWV) and leaf spots which will cause significant yield loss. The most sustainable, economical and eco-friendly solution for managing peanut diseases is development of improved cultivars with high level of resistance. We developed a recombinant inbred line population from the cross between SunOleic 97R and NC94022, named as the S-population. An improved genetic linkage map was developed for the S-population with 248 marker loci and a marker density of 5.7 cM/loci. This genetic map was also compared with the physical map of diploid progenitors of tetraploid peanut, resulting in an overall co-linearity of about 60% with the average co-linearity of 68% for the A sub-genome and 47% for the B sub-genome. The analysis using the improved genetic map and multi-season (2010–2013) phenotypic data resulted in the identification of 48 quantitative trait loci (QTLs) with phenotypic variance explained (PVE) from 3.88 to 29.14%. Of the 48 QTLs, six QTLs were identified for resistance to TSWV, 22 QTLs for early leaf spot (ELS) and 20 QTLs for late leaf spot (LLS), which included four, six, and six major QTLs (PVE larger than 10%) for each disease, respectively. A total of six major genomic regions (MGR) were found to have QTLs controlling more than one disease resistance. The identified QTLs and resistance gene-rich MGRs will facilitate further discovery of resistance genes and development of molecular markers for these important diseases. [ABSTRACT FROM AUTHOR]

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. Abstract: 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. [ABSTRACT FROM AUTHOR]

Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality. [ABSTRACT FROM AUTHOR]

Key Message: The candidate gene AhLBA1 controlling lateral branch angel of peanut was fine-mapped to a 136.65-kb physical region on chromosome 15 using the BSA-seq and QTL mapping. Lateral branch angel (LBA) is an important plant architecture trait of peanut, which plays key role in lodging, peg soil penetration and pod yield. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for LBA in peanut. In this project, a mapping population was constructed using a spreading variety Tifrunner and the erect variety Fuhuasheng. Through bulked segregant analysis sequencing (BSA-seq), a major gene related to LBA, named as AhLBA1, was preliminarily mapped at the region of Chr.15: 150-160 Mb. Then, using traditional QTL approach, AhLBA1 was narrowed to a 1.12 cM region, corresponding to a 136.65-kb physical interval of the reference genome. Of the nine genes housed in this region, three of them were involved in hormone metabolism and regulation, including one "F-box protein" and two "2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase (2OG oxygenase)" encoding genes. In addition, we found that the level of some classes of cytokinin (CK), auxin and ethylene showed significant differences between spreading and erect peanuts at the junction of main stem and lateral branch. These findings will aid further elucidation of the genetic mechanism of LBA in peanut and facilitating marker-assisted selection (MAS) in the future breeding program. [ABSTRACT FROM AUTHOR]

Genomic regions governing water deficit stress tolerance were identified in peanut using a recombinant inbred line (RIL) population derived from an elite variety TMV 2 and its narrow leaf mutant TMV 2-NLM, which was evaluated over six-seasons at Dharwad (non-stress) and Tirupati (water-stress) in India. Stress condition could differentiate the RILs much better than the non-stress condition for the physiological traits. A linkage map with 700 markers was used to identify the quantitative trait loci (QTLs). Three sets of best linear unbiased predictions (BLUPs) were estimated for the drought tolerance traits for the rainy and post-rainy seasons at Dharwad and post-rainy seasons at Tirupati, and employed for single marker analysis, composite interval mapping and multiple QTL mapping. Of the 305 significant marker-trait associations for the 11 traits, only 21 were of major effect for pod yield per plant (PYPP), specific dry weight at 70 days after sowing (SDW_70) and specific leaf area at 70 DAS (SLA_70). Three major main effect QTLs were identified for PYPP with the highest phenotypic variance explained (PVE) of 10.5%. Nine QTLs with the highest PVE of 18.4% were identified for SDW_70, of which four QTLs were also governing SLA_70 with the highest PVE of 15.7%. A few of them were also involved in epistatic interactions, and formed multiple QTL mapping models. Five major QTLs for SDW_70 were stable over both the locations. Candidate genes with SNPs and AhMITE1 insertion were identified for the major QTL regions. A rare nonsynonymous SNP at Ah02_1558700 within the gene ArahyW1P0U6 governing PYPP was detected. Functional analysis of these candidate genes may be useful for future genetic modifications in addition to validating and using the linked markers for improving drought tolerance in peanut. [ABSTRACT FROM AUTHOR]

[Display omitted] • The study presents a large-scale SNP data set from the whole-genome resequencing of 203 cultivated peanut accessions. • Population structure and demographic history are investigated. • Signatures of selection occurred during peanut improvement breeding are demonstrated. • Candidate genes associated with seed traits are identified by GWAS and transgenic experiments. Cultivated peanut (Arachis hypogaea L.) is an important oil crop for human nutrition and is cultivated in >100 countries. However, the present knowledge of its genomic diversity, evolution, and loci related to the seed traits is limited. Our study intended to (1) uncover the population structure and the demographic history of peanuts, (2) identify signatures of selection that occurred during peanut improvement breeding, and (3) detect and verify the functions of candidate genes associated with seed traits. We explored the population relationship and the evolution of peanuts using a largescale single nucleotide polymorphism dataset generated from the genome-wide resequencing of 203 cultivated peanuts. Genetic diversity and genomic scan analyses were applied to identify selective loci for genomic-selection breeding. Genome-wide association studies, transgenic experiments, and RNA-seq were employed to identify the candidate genes associated with seed traits. Our study revealed that the 203 resequenced accessions were divided into four genetic groups, consistent with their botanical classification. Moreover, the var. peruviana and var. fastigiata subpopulations have diverged to a greater extent than the others, and var. peruviana may be the earliest variant in the evolution from tetraploid ancestors. A recent dramatic expansion in the effective population size of the cultivated peanuts ca. 300–500 years ago was also noted. Selective sweeps underlying quantitative trait loci and genes of seed size, plant architecture, and disease resistance coincide with the major goals of improved peanut breeding compared with the landrace and cultivar populations. Genome-wide association testing with functional analysis led to the identification of two genes involved in seed weight and seed length regulation. Our study provides valuable information for understanding the genomic diversity and the evolution of peanuts and serves as a genomic basis for improving peanut cultivars. [ABSTRACT FROM AUTHOR]

Heterogeneous inbred families segregating for rust resistance were identified from the two crosses involving susceptible ( TAG 24 and TG 26) and resistant ( GPBD 4) varieties of peanut. Rust-resistant (less than score 5) and rust-susceptible (more than score 5) plants were identified in each HIF and evaluated under rust epiphytotic conditions. The set of plants belonging to the same HIF, but differing significantly in rust resistance, not in other morphological and productivity traits, was regarded as near-isogenic lines (NILs). Largely, rust-resistant NILs had GPBD 4-type allele, and susceptible NILs carried either TAG 24 or TG 26-type allele at the three SSR loci ( IPAHM103, GM1536 and GM2301) linked to a major genomic region governing rust resistance. Comparison of the remaining genomic regions between the NILs originating from each of the HIFs using transposon markers indicated a considerably high similarity of 86.4% and 83.1% in TAG 24 × GPPBD 4 and TG 26 × GPBD 4, respectively. These NILs are useful for fine mapping and expression analysis of rust resistance. [ABSTRACT FROM AUTHOR]

Spanish bunch groundnut varieties occupy most of the cultivated area in Asia and Africa, and these varieties lack required 2-3 weeks of fresh seed dormancy (FSD) hampering kernel quality. Genomic breeding can help to improve commercial groundnut cultivars for FSD in a shorter time with greater precision. In this regard, a recombinant inbred line (RIL) population from the cross ICGV 02266 (non-dormant) × ICGV 97045 (dormant) was developed and genotyped with a 5 K mid-density genotyping assay. A linkage map was constructed with 325 SNP loci spanning a total map length of 2335.3 cM and five major QTLs were identified on chromosomes Ah01, Ah11, Ah06, Ah16 and Ah17. Based on differential gene expression using transcriptomic information from dormant (Tifrunner) and non-dormant (ICGV 91114) genotypes, histone deacetylases, histone-lysine N-methyltransferase, cytochrome P450, protein kinases, and ethylene-responsive transcription factor were identified as key regulators involved in the hormonal regulation of dormancy. Six Kompetitive Allele Specific PCR (KASP) markers were successfully validated in the diverse panel including selected RILs of the same population and germplasm lines. These validated KASP markers could facilitate faster breeding of new varieties with desired dormancy using marker-assisted early generation selection. [ABSTRACT FROM AUTHOR]

Background: Aflatoxin contamination caused by Aspergillus flavus is a major constraint to peanut industry worldwide due to its toxicological effects to human and animals. Developing peanut varieties with resistance to seed infection and/or aflatoxin accumulation is the most effective and economic strategy for reducing aflatoxin risk in food chain. Breeding for resistance to aflatoxin in peanut is a challenging task for breeders because the genetic basis is still poorly understood. To identify the quantitative trait loci (QTLs) for resistance to aflatoxin contamination in peanut, a recombinant inbred line (RIL) population was developed from crossing Zhonghua 10 (susceptible) with ICG 12625 (resistant). The percent seed infection index (PSII), the contents of aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) of RILs were evaluated by a laboratory kernel inoculation assay. Results: Two QTLs were identified for PSII including one major QTL with 11.32–13.00% phenotypic variance explained (PVE). A total of 12 QTLs for aflatoxin accumulation were detected by unconditional analysis, and four of them (qAFB1A07 and qAFB1B06.1 for AFB1, qAFB2A07 and qAFB2B06 for AFB2) exhibited major and stable effects across multiple environments with 9.32–21.02% PVE. Furthermore, not only qAFB1A07 and qAFB2A07 were co-localized in the same genetic interval on LG A07, but qAFB1B06.1 was also co-localized with qAFB2B06 on LG B06. Conditional QTL mapping also confirmed that there was a strong interaction between resistance to AFB1 and AFB2 accumulation. Genotyping of RILs revealed that qAFB1A07 and qAFB1B06.1 interacted additively to improve the resistance to both AFB1 and AFB2 accumulation. Additionally, validation of the two markers was performed in diversified germplasm collection and four accessions with resistance to aflatoxin accumulation were identified. Conclusions: Single major QTL for resistance to PSII and two important co-localized intervals associated with major QTLs for resistance to AFB1 and AFB2. Combination of these intervals could improve the resistance to aflatoxin accumulation in peanut. SSR markers linked to these intervals were identified and validated. The identified QTLs and associated markers exhibit potential to be applied in improvement of resistance to aflatoxin contamination. [ABSTRACT FROM AUTHOR]