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In plant breeding, selecting cross‐combinations that are more likely to result in superior lines for cultivar development is critical. This step, however, is subjective with decisions being based on available genomic and phenotypic data for prospective parents. Genomic prediction (GP) provides new opportunities to accelerate genetic gain for a target trait by identifying superior crosses through simulation of progeny performance. In this context, this study deployed GP using the phenotype and genotype of potential parents to predict the progeny genetic variance (VG) and means of overall, inferior 10%, and superior 10% (μ, μip, and μsp, respectively). This retrospective experimental design investigated whether the crosses that produced superior soft red winter wheat breeding lines would have been made if progeny simulations had guided crossing decisions of breeding programs. Here, data from historical wheat breeding lines were used to train GP models and predict VGand means for yield, test weight, heading date, and plant height for all combinations of 217 parents. Predicted and observed data for 670 lines derived from biparental crosses were compared to assess the accuracy of progeny simulations, and low‐to‐moderate prediction accuracy was observed for the four traits (0.25–0.52). Of the pedigrees that produced lines that were selected and advanced into later stage nurseries, 76% were predicted to give rise to progeny with above‐average yield. The moderate correlation found between predicted progeny means and observed line per se performance justifies using cross‐combination prediction as a tool to reduce crossing number and focus on segregating populations that harbor future cultivars. In plant breeding, selecting parents to be crossed is critical for developing superior progeny.Historical winter wheat data were used to assess the usefulness of genomic prediction for parental selection.Predicted yield and SunGrains breeders’ assessment and selection largely agreed.Simulated progeny performance could allow breeders to focus on the most promising crosses.

Wild relatives comprise a diverse genetic source from which to introduce beneficial alleles for peanut breeding. However, when using wild species for breeding, unadapted agronomic characteristics are often co‐inherited along with favorable traits. Previously, an advanced backcross population was developed from a cross between Arachis hypogaeaand the wild‐derived induced allotetraploid (Arachis batizocoi× Arachis stenosperma)4xto incorporate nematode resistance genes into elite peanut. We observed additional wild alleles unintentionally inherited throughout the genome, possibly causing variation in several pod and seed characteristics. To identify the wild introgressions controlling the variation in pod constriction (PC), a critical trait for peanut's acceptability and marketability, we performed an association analysis using 419 SNPs and phenotypic data of 72 BC3F2/3families. An introgression on the top of chromosome B08 (pod constriction‐quantitative trait locus [PC‐QTL], 3.7 Mbp) derived from A. batizocoiwas found to be controlling 47.3% of the PC variation. To confirm the PC‐QTL, six BC3F4families harboring the wild loci in a homozygous or heterozygous state were selected and used for segregation analysis. All progenies from the backcross families carrying the homozygous allele had severely constricted pods, whereas progenies from families with the heterozygous allele were segregated for PC. Finally, analyses using end‐point genotyping with four linked SNP assays confirmed the association of the PC‐QTL with PC. The present work studied PC and developed DNA markers to assist the selection against constricted pods while retaining the new and beneficial wild‐derived genes. In peanut, pod and seed traits are important for yield and quality.When incorporating beneficial traits from wild germplasm, unadapted wild pod and seed traits are also inherited.A major pod constriction quantitative trait locus was discovered in a backcross population harboring wild‐derived segments.Molecular markers developed and validated can be used for selection against wild‐type deep pod constriction.

Peanut (Arachis hypogaeaL.) root‐knot nematode (PRKN) Meloidogyne arenariais a very destructive pathogen to which most peanut cultivars are highly susceptible. Current peanut cultivars rely on a single locus for PRKN resistance incorporated from the wild relative A. cardenasiiKrapov. & W.C. Greg., that could be overcome as a result of the emergence of new nematode populations. Thus, new sources of resistance are continually needed. A new and strong resistance has been found in the wild diploid relative, A. stenospermaKrapov. & W.C. Greg. Arachis stenosperma‐derived quantitative trait loci (QTL) were described on chromosomes A02 and A09 and reduced nematode development by up to 98.2%. In order to validate these resistance segments, this study screened for PRKN resistance in BC2F1lines and correlated with molecular genotypes. Here, six BC2F1s carrying chromosome introgressions in A02 and/or A09, showed strong resistance while one line was susceptible. Both phenotype and genotype data allowed us to validate and delineate the chromosomal segments in chromosomes A02 and A09 to ∼8.5Mbp and ∼6.5Mbp regions on the bottom of each, respectively. Within the QTL on A02 and top middle of both chromosomes A02 and A09 there are R‐gene clusters, often implicated in pathogen resistance. We have provided validation of these key resistance QTL that can be used to inform breeding via marker selection and insights into the functional basis of resistance provided by the wild peanut relative A. stenosperma. Validation of peanut root‐knot nematode resistance incorporated in second generation of backcross lines.Incorporation of peanut root‐knot nematode resistance QTL from Arachis stenosperma.Towards the development of root‐knot nematode (Meloidogyne arenaria)‐resistant peanut cultivars.

Like many other crops, the cultivated peanut (Arachis hypogaeaL.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaeaover other diploid Arachisspecies cultivated by humans.