Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut

Abstract

Peanut (Arachis hypogaea; 2n = 4x = 40) is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facilitate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide polymorphisms (SNPs) were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic regions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone positive selection. These observations provide key insights on the inclusion of new genetic diversity in cultivated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.

Keywords: Arachis hypogaea; groundnut; single nucleotide polymorphism.

Figure 1

Tetrasomic Markers in Tetraploid Germplasm and Segregating in RIL Populations. (A and B) Tetrasomic segregation in tetraploid germplasm where Tifrunner and NC3033 are homozygous quadriplex and nulliplex (A) and segregation in the RIL population showing tetrasomic segregation (B). (C and D) Tetrasomic segregation in tetraploid germplasm where Tifrunner and NC3033 are monomorphic (C) and RIL population showing tetrasomic recombination in one individual (D).

Figure 2

Tetrasomic Markers in Tetraploid Germplasm and Segregating in RIL Populations. (A and B) Tetrasomic segregation in tetraploid germplasm where Tifrunner and NC3033 are homozygous quadriplex and duplex (A) and segregation in the RIL population showing disomic segregation (B). (C and D) Tetrasomic segregation in tetraploid germplasm where Tifrunner and NC3033 are quadriplex and nulliplex (C) and the RIL population showing tetrasomic recombination (D).

Figure 3

Tracking Changes in Recombination and Genetic Diversity in US Runner Genotypes. (A) Recombination events/number of possible events for each chromosome grouped by breeding cycle. (B) Frequency of all polymorphic markers (left panel) observed in the populations and 1% of the simulated distribution of simulated polymorphism due to genetic drift. The right panel shows markers unique to only one ancestor. (C) First two principal components of genetic diversity between cultivars grouped by breeding cycle and major germplasm introduction.

Figure 4

Analysis of Breeding Trios Uncovers Signatures of Selection. Log transformed p value of the binomial exact test of directed selection versus no selection by physical position of A. duranensis (A genome, left panel) and A. ipaensis (B genome, right panel) pseudomolecules.

Figure 5

Haplotype Frequency and Diversity on Chromosome B09. Top three panels: Haplotype frequency was determined in the USDA mini core collection in 20 marker sliding windows moving five marker intervals. The top eight haplotypes in terms of frequency along with the haplotype from PI203396 were then assessed for frequency in the eight main ancestors (top), cultivars released in cycles four, five, and six (top middle), and cultivars released in cycles seven and eight (top bottom). Line graphs below show the number of unique haplotypes in the four populations, the ratio of unique haplotypes to population size, and genetic diversity normalized to the estimated A. hypogaea haplotype diversity from the mini core collection as log₂(π population/π mini core).