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Key message: Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era. [ABSTRACT FROM AUTHOR]

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. [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]

Iron deficiency chlorosis (IDC) under calcareous and alkaline soils is a significant abiotic stress affecting the growth and yield of peanut. In this study, the genomic regions governing IDC tolerance were mapped using a recombinant inbred line (RIL) population derived from TMV 2 (susceptible to IDC) and TMV 2-NLM (tolerant to IDC), which was phenotyped during the rainy seasons of 2019 and 2020 in the iron-deficient calcareous plots. The best linear unbiased prediction (BLUP) values for IDC tolerance traits like visual chlorotic rating (VCR), and SPAD chlorophyll meter reading (SCMR) were used for QTL analysis along with a genetic map carrying 700 GBS-derived SNP, AhTE and SSR markers. In total, 11 and 12 main-effect QTLs were identified for VCR and SCMR, respectively. Among them three QTLs were major with the phenotypic variance explained (PVE) of 10.3–34.4% for VCR, and two QTL were major for SCMR with PVE of 11.5–11.7%. A region (159.3–178.3 cM) on chromosome Ah13 carrying two QTLs (one each for VCR and SCMR) was consistent with the previous report. A SNP marker, Ah14_138037990 identified from single marker analysis for VCR was located in the intronic region of the gene Arahy.QA0C1, which is important for protein-binding. Overall, this study identified new QTLs and also validated QTL for IDC tolerance. These genomic resources could be useful for genomics-assisted breeding of peanut for IDC tolerance. [ABSTRACT FROM AUTHOR]