Pedigree reconstruction for triploid apple cultivars using single nucleotide polymorphism array data

Abstract

Many economically, culturally, and historically important apple cultivars are triploids, which have three copies of each chromosome instead of the more typical two copies in diploids. Despite their prevalence and importance, there have been conflicting reports regarding their origin and their ability to beget diploids. New genetic analysis methodologies outlined in this study have clarified the genetic origin of triploid apple cultivars and suggest that triploidy has been a dead end in historic apple pedigrees.The specific results of this study have resolved the pedigrees of many cultivars, including the famous English cultivar Cox's Orange Pippin and the oldest known US cultivar Roxbury Russet. Summary• In apple (Malus  domestica), most cultivars are diploid, though a sizeable number are triploids, which tend to be stronger growing, more robust, and bear larger fruit.However, triploidy is also associated with strongly reduced fertility. Some recorded pedigrees for historical apple cultivars include triploids as parents of diploids, despite this reputation of poor fertility. This information, coupled with some initiatives using triploids in breeding efforts, result in confusion about how possible or common it is for triploids to be parents of diploid offspring. To date, no studies have systematically evaluated and identified pedigrees of triploid apple cultivars to resolve these contradictions.• Here, we describe a method to make triploid genotype calls using Illumina Infinium single nucleotide polymorphism (SNP) array data through a novel Python script: ploidyClassifier. SNP data for 219 unique triploids was compared alongside 2498 unique diploid apple accessions to conduct pedigree reconstruction.• Unreduced gamete-donating parents were identified for over half of the triploid accessions. From those, reduced gamete-donating parents were identified for nearly half. Full or partial pedigrees for many classic triploids were uncovered, including that of the oldest known American cultivar, 'Roxbury Russet'. All tested pedigrees from literature that listed triploids as parents of diploids were deemed

Apple and banana fruits produce anteiso- and iso-branched-chain esters from newly synthesized precursors

“…To investigate the population genetics of citramalate synthase, and thus branched-chain esters in apples, we sequenced the consequential single nucleotide polymorphism of citramalate synthase from thirty-two cultivars within the USDA Geneva Malus Core Collection that have been previously identified as being derived from ‘Cox’s Orange Pippin’ (Migicovsky, et al, 2021; Muranty, et al, 2020; Howard, et al, 2023). Given our population definitions (see Supplemental Text), we would expect 29.1% of ‘Cox’s Orange Pippin’s offspring to be homozygous recessive if no selection is occurring, however, only three cultivars (9.4%) were homozygous recessive ( Fig.…”

“…The parent population (from Sugimoto et al (2021)) and offspring population were mutually exclusive save for ‘James Grieves’, however this cultivar has been identified as being an offspring of ‘Cox’s Orange Pippin’ and was thusly sequestered to the offspring population (Muranty, et al, 2020). Two cultivars, ‘Cherry Cox’ and ‘Potter Cox’, were identified as being sport mutations of ‘Cox’s Orange Pippin’ whereas another two cultivars, ‘Margil’ and ‘Rosemary Russet’, have been determined to be the parents of ‘Cox’s Orange Pippin’ (Muranty, et al, 2020) (Howard, et al, 2023). The sports (both homozygous recessive), and parents (both heterozygous) were removed from further analysis.…”

A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17

“…Given the pivotal role of centromeres in mitosis and meiosis ( Pluta et al., 1995 ), it is reasonable to infer that this duplicated region encompasses the centromeric region. Triploids in plant species often arise from the fusion of a reduced gamete ( n ) and an unreduced gamete (2 n ) ( Pelé et al., 2018 ; Howard et al., 2023 ). Unreduced gametes are produced by failure of disjunction of homologous chromosomes in meiosis.…”

Fruit in focus: A sampler platter of research

“…In Diaz‐Garcia and Padilla‐Ramírez (2023), the authors examine phenotypic and genomic diversity in guava ( Psidium guajava ), using this information to shed light on the evolutionary history and breeding potential of this crop. In Howard et al (2023), a novel method is introduced to identify triploid apple cultivars using single nucleotide array data, which is then applied to perform pedigree reconstruction and parentage analysis. These works from the special collection quantify diversity across scales, from the nucleotide to the overall shape of a fruit, capturing the immense amount of phenotypic and genomic diversity found in fruit‐bearing plants.…”