Construction of a high-density linkage map and QTL analysis for pistil abortion in apricot (Prunus armeniaca L.)

Abstract

A high-density genetic map of apricot (Prunus armeniaca L.) was constructed using an F1 population constructed by crossing two main Chinese cultivars ‘Chuanzhihong’ and ‘Luotuohuang’, coupled with a recently developed reduced representation library (RRL) sequencing. The average sequencing depth was 38.97 in ‘Chuanzhihong’ (female parent), 33.05 in ‘Luotuohuang’ (male parent), and 8.91 in each progeny. Based on the sequencing data, 12 451 polymorphic markers were developed and used in the construction of the genetic linkage map. The final map of apricot comprised eight linkage groups, including 1991 markers, and covered 886.25 cM of the total map length. The average distance between adjacent markers was narrowed to 0.46 cM. Gaps larger than 5 cM only accounted for <0.33%. To our knowledge, this map is the densest genetic linkage map that is currently available for apricot research. It is a valuable linkage map for quantitative trait loci (QTLs) identification of important agronomic traits. Moreover, the high marker density and well-ordered markers that this linkage map provides will be useful for molecular breeding of apricot as well. In this study, we applied this map in the QTL analysis of an important agronomic trait, pistil abortion. Several QTLs were detected and mapped respectively to the middle regions of LG5 (51.005∼59.4 cM) and LG6 (72.884∼76.562 cM), with nine SLAF markers closely linked to pistil abortion. The high-density genetic map and QTLs detected in this study will facilitate marker-assisted breeding and apricot genomic study.

Mapping Quantitative Trait Loci Associated With Graft (In)Compatibility in Apricot (Prunus armeniaca L.)

“…In this report, we utilized the SBG technology to generate extensive dataset of the SNP markers distributed throughout the apricot (Prunus armeniaca) genome. Parental maps constructed for the "Mo × Pa" cross provided sufficient marker density for downstream QTL analyses and were comparable with recently released saturated genetic maps for apricot cross segregating for pistil abortion trait (Zhang et al, 2019). Similar marker density was reported in other Prunus species such as peach (Bielenberg et al, 2015), cherry (Klagges et al, 2013;Calle et al, 2018), and Japanese plum (Salazar et al, 2017).…”

“…In fruit trees, genotyping by sequencing to date was conducted in apple (Nocker and Gardiner, 2014), raspberry (Ward et al, 2013), cherry (Guajardo et al, 2015), peach (Bielenberg et al, 2015), Japanese plum (Salazar et al, 2017(Salazar et al, , 2019, and Prunus rootstock germplasm collections (Guajardo et al, 2020), generating SNPs of sufficient quality and quantity to be of utility in genetic mapping. In apricot, high-density genetic map was constructed and used for mapping pistil abortion, an important agronomic trait decreasing the yield in production (Zhang et al, 2019). However, the genetic control of GI remains poorly understood mainly because of a lack of hybrid crosses, segregating for the trait.…”

Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci Linked to Fruit Quality Traits in Apricots Using Specific-Locus Amplified Fragment Sequencing

“…Specific-locus amplified fragment sequencing (SLAF-seq) is a high-throughput technique widely adopted for the development of SNP markers in different species, such as the genetic map of peaches spanning 1098.79 cM with an average distance of 0.17 cM between adjacent markers ( Shi et al, 2020 ) and the map of tea covering a distance of 3,965 cM with an average inter-locus distance of 1.0 cM ( Ma et al, 2015 ). Zhang et al (2019) constructed a high-density linkage map using the SLAF markers, and detected several QTLs for pistil abortion.…”

Transcriptome analysis insight into ethylene metabolism and pectinase activity of apricot (Prunus armeniaca L.) development and ripening

“…The Q30 base percentage was greater than 93%, and the percentage of G and C bases among the total bases was 45.85–46.29% (Table 1 ). The reference gene source was Prunus_armeniaca, and the reference genome version was parmeniaca_v1.0 2 . The clean reads of each sample were compared with the designated reference genome, and the alignment rate ranged from 89.53 to 92.95%.…”

“…fruit is rich in a variety of nutrients, including carotenoids, polyphenols, ascorbic acid and numerous trace elements 1 . Apricot has a high nutritional content, can be processed into a variety of food products and has become an important fruit worldwide 2 . Apricot fruit is a respiratory climacteric fruit 3 .…”