Identification of loci for single/double flower trait by combining genome‐wide association analysis and bulked segregant analysis in peach (Prunus persica)

Abstract

Background Peach is a typical perennial fruit crop that can be categorized both as an ornamental and edible crop. Double flower is an important appearance trait, in which breeders are pursuing in high‐quality ornamental peach breeding. The single/double flower character in peach is controlled by one gene, Dl, and the underlying genetic mechanism is unknown. Objective In this study, we explored the genetic basis of single/double flower trait in peach in a genome‐wide association study using 1 042 687 SNPs characterized in 201 accessions. Methodology Four loci were identified to be significantly associated with the trait on chromosomes (Chr.) 1, 2 and 6. Besides, the bulked segregant analysis (BSA) was performed with two DNA bulks (single and double flower pool) from the F1 population plants of a cross 'Juhuatao' × 'Honggengansutao'. Results We found a genomic region on Chr. 2 by the BSA, which overlapped the association peak on Chr. 2 in the GWAS—denoted as a region harbouring Dl. Finally, a candidate gene was identified by expression analysis of different plant tissues. Conclusion Our results provide insights into the genetic basis of flower shape and might facilitate marker‐assisted selection breeding for ornamental peach.

Preliminary Identification of Key Genes Controlling Peach Pollen Fertility Using Genome-Wide Association Study

“…In the past few decades, for the peach pollen fertility/sterility trait, the top region of Chr.06 (0–7.52 Mb) was characterized as a hotspot by using genetic mapping in different hybrid populations, but it remained difficult to focus on specific genes as the SSR markers used were employed at a low density [ 24 , 25 , 26 , 27 ]. With the capabilities of sequencing technologies, high-density molecular markers have been widely adopted in genetic basis dissection [ 30 , 31 , 32 , 33 , 34 , 35 , 36 ]. In our study, using the high-quality SNPs generated from the re-sequencing data of 201 peach accessions, a significant association peak was detected at Chr.06: 2,116,368 bp ( Figure 3 ), which is in accordance with the previous genetic mapping results but displays largely improved precision, allowing follow-up candidate gene identification ( Table 1 ).…”

“…The whole-genome re-sequencing of the 201 peach accessions was completed in our previous work [ 34 ]. The library insert size was 500 bp, and the pair-end read size was 150 bp.…”

“…As an alternative approach to conventional genetic mapping, the genome-wide association study (GWAS) has rapidly come into focus for the genetic dissection of complex traits by exploiting the linkage disequilibrium (LD) present among individuals from natural populations or germplasm collections, offering advantages including increased resolution, a reduced research period and improved allele number detection [ 28 , 29 ]. Several comprehensive GWAS projects have shed light on the genetic basis of important agronomic traits, such as fruit size and shape, fruit sugar and acid content, fruit texture, and chilling requirement, and have provided us with reliable markers for efficient genomic selection [ 30 , 31 , 32 , 33 , 34 , 35 , 36 ].…”

SMRT and Illumina RNA-Seq Identifies Potential Candidate Genes Related to the Double Flower Phenotype and Unveils SsAP2 as a Key Regulator of the Double-Flower Trait in Sagittaria sagittifolia

“…Double flowers, which are characterized by the excessive development of petals, are important in ornamental flowers because they are considered to be more attractive in gardens than their normal counterparts. Breeders have selected the double flower phenotype in many varieties, such as gerbera daisy (Gerbera jamesonii), carnations (Dianthus caryophyllus), and peach (Prunus persica) [1][2][3]. In the past few decades, flower development has been widely studied in arabidopsis (Arabidopsis thaliana) and snapdragons (Antirrhinum majus), and the ABC model has been established to explain the characteristics of floral organs [4][5][6].…”

“…During the development of A. thaliana flowers, the inhibition of euAP2 gene by miR172 is critical to maintain the certainty of flower organs [21]. In peach (Prunus persica) and rose, a mutant allele of the AP2 transcription factor was found to be primarily related to double flowers, and this transcription factor plays a conserved role in the regulation of flower patterns and development transformation [3,17]. The ap2 mutant has an abnormal flower phenotype in A. thaliana, including loss of petals and homologous transformation of sepals to carpels.…”