Fine-Mapping the Branching Habit Trait in Cultivated Peanut by Combining Bulked Segregant Analysis and High-Throughput Sequencing

Abstract

The growth habit of lateral shoots (also termed “branching habit”) is an important descriptive and agronomic character of peanut. Yet, both the inheritance of branching habit and the genetic mechanism that controls it in this crop remain unclear. In addition, the low degree of polymorphism among cultivated peanut varieties hinders fine-mapping of this and other traits in non-homozygous genetic structures. Here, we combined high-throughput sequencing with a well-defined genetic system to study these issues in peanut. Initially, segregating F2 populations derived from a reciprocal cross between very closely related Virginia-type peanut cultivars with spreading and bunch growth habits were examined. The spreading/bunch trait was shown to be controlled by a single gene with no cytoplasmic effect. That gene was named Bunch1 and was significantly correlated with pod yield per plant, time to maturation and the ratio of “dead-end” pods. Subsequently, bulked segregant analysis was performed on 52 completely bunch, and 47 completely spreading F3 families. In order to facilitate the process of SNP detection and candidate-gene analysis, the transcriptome was used instead of genomic DNA. Young leaves were sampled and bulked. Reads from Illumina sequencing were aligned against the peanut reference transcriptome and the diploid genomes. Inter-varietal SNPs were detected, scored and quality-filtered. Thirty-four candidate SNPs were found to have a bulk frequency ratio value >10 and 6 of those SNPs were found to be located in the genomic region of linkage group B5. Three best hits from that over-represented region were further analyzed in the segregating population. The trait locus was found to be located in a ~1.1 Mbp segment between markers M875 (B5:145,553,897; 1.9 cM) and M255 (B5:146,649,943; 2.25 cM). The method was validated using a population of recombinant inbreed lines of the same cross and a new DNA SNP-array. This study demonstrates the relatively straight-forward utilization of bulk segregant analysis for trait fine-mapping in the low polymeric and heterozygous germplasm of cultivated peanut and provides a baseline for candidate gene discovery and map-based cloning of Bunch1.

Genetic insight and mapping of the pod constriction trait in Virginia-type peanut

“…On the basis of the expected and observed frequencies of VPC, the χ 2 test was found to not be significantly different from a 1:1 ratio ( p = 0.79). VPC was also evaluated among Hanoch × Harari based F 1 and F 2 populations (a detailed description of those populations can be found in Kayam et al [ 16 ]). VPC segregated at a rate of 5:0 for slight: deep among the F 1 plants and at a rate of approximately 3:1 ( p = 0.39) among the F 2 generation (Table 2 ).…”

“… df = 1. *The observed ratio is not significantly different from the expected ratio at p = 0.05 F 1 and F 2 plants were grown as described at [ 16 ] …”

“…In addition to the RIL population, F 2 generation that was derived from the same cross was validated for PC in field trial based on individual plants. All field procedures for this population were previously described [ 16 ].…”

The PIN-FORMED Auxin Efflux Carriers in Plants

“…In Medicago truncatula , PINs have a role in forming the root nodules in an auxin-dependent manner by silencing MtPIN2 / 3 / 4 , which reduced the number of nodules [ 44 , 45 , 179 ]. In cotton, PIN proteins have a role in regulating fiber growth, and the heterologous overexpression of GhPIN1a_Dt , GhPIN6_At and GhPIN8_At in Arabidopsis changed the number and size of leaf trichomes [ 41 ]. In rice, OsPIN2 was expressed in epidermal and cortex cells of roots, and it regulated the gravitropic responses and root system architecture [ 180 ].…”

Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton

“…Compared with genetic mapping, The NGS is a faster and reliable method for mapping [64]. Nevertheless, one mixed pool typically contains approximately 20-100 individuals generally maps the target region at a Mb-level interval [65][66][67][68][69]. Because of insu cient meiotic recombination events, we still have to perform ne mapping or use omics methods such as RNA-seq to further screen the candidate genes [70,71].…”