Abundant Microsatellite Diversity and Oil Content in Wild Arachis Species

Abstract

The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.

Genetic Diversity and Population Structure of Miscanthus sinensis Germplasm in China

“…The large difference of genetic diversity between the cultivated varieties and the wild germplasm could likely be attributed to domestication events that greatly reduced genetic diversity in popular varieties [34]–[36]. Evaluation of the genetic diversity in wild germplasm is crucial for efficient exploitation of the valuable alleles present in the wild resources, which has been demonstrated in previous studies for rice, maize and sweet sorghum [34], [37]–[42].…”

Utilizing Wild Species for Peanut Improvement

“…Foncéka et al (2012) produced populations derived from crosses of cultivar Fleur 11 and an amphidiploid (A. ipaënsis ´ A. duranensis) 4x , and Fávero et al (2006) identified QTLs associated with days to flowering, plant architecture, pod and seed morphology, and yield components. Huang et al (2012) found significant variation for oil content among Arachis species and associated three alleles for higher oil content than in cultivated peanut using SSR markers. Huang et al (2012) found significant variation for oil content among Arachis species and associated three alleles for higher oil content than in cultivated peanut using SSR markers.…”

“…The wild species alleles contributed positive variation to several agronomic traits such as number of flowers, seed and pod number per plant, and length, size, and maturity of pods. Huang et al (2012) found significant variation for oil content among Arachis species and associated three alleles for higher oil content than in cultivated peanut using SSR markers. By comparing QTLs obtained under well-watered and water-limited conditions, they discovered markers for drought tolerance and for pod and seed number; the alleles were attributed to the wild parents.…”

Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

“…It was concluded that a genetic bottleneck occurring as a result of the polyploidization event, coupled with a self-pollinating reproductive system, and the use of a few elite breeding lines with little exotic germplasm in breeding programs, has resulted in a narrow genetic base of peanut cultivars. Natural gene exchange between wild diploid species and cultivated peanut may have been limited due to genomic rearrangement as well as differences in ploidy levels (Soltis and Soltis 1999; Huang et al 2012). Since then, >10,000 SSR markers have been identified in peanut, many solely among wild species, but few SSR marker maps possess 200 or more SSR markers, again suggesting low genetic variability in the cultivated species.…”