Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus

Dougherty, Laura; Singh, R. N.; Brown, Susan K.; Dardick, Chris; Xu, Kenong

doi:10.1093/jxb/erx490

Cited by 32 publications

(50 citation statements)

References 74 publications

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“…Since that time, weeping architectures in several tree species have been shown to segregate as single gene traits. A weeping phenotype in apple has been linked to a single dominant locus, while two distinct eastern redbud weeping phenotypes have been linked to recessive loci, and weeping phenotypes in chestnut have been linked to both recessive and dominant loci (18)(19)(20)(21)(22). Weeping in Japanese apricot (Prunus mume) was shown to be recessive and mapped to a region on linkage group 7 (23).…”

Section: Significancementioning

confidence: 99%

Loss of a highly conserved sterile alpha motif domain gene ( WEEP ) results in pendulous branch growth in peach trees

Hollender

Pascal

Tabb

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene,, having a 1.8-Kb deletion spanning the 5' end. This gene, dubbed , was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity perception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications.

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Section: Significancementioning

confidence: 99%

Loss of a highly conserved sterile alpha motif domain gene ( WEEP ) results in pendulous branch growth in peach trees

Hollender

Pascal

Tabb

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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“…Pedigree-based quantitative trait locus (QTL) mapping and genome-wide association studies are powerful tools for mapping both qualitative and quantitative traits (Hamblin et al, 2011;Longhi et al, 2012;Farneti et al, 2017;Ye et al, 2017). Recently, bulk segregant analysis (BSA)-seq, a next-generation sequencing (NGS)-based QTL mapping strategy analysis, in which two phenotypically distinct subpopulations (bulks) (BSA extremity bulks) of recombinant progeny (segregants) are isolated from a genetic cross and genotyped, has proved successful for rapidly mapping genes in several cereal and vegetable plants (Trick et al, 2012;Takagi et al, 2013;Huo et al, 2016;Dougherty et al, 2018). By combining MapQTL and BSA-seq, an AAA ATPase gene CsARN6.1 and the Ef1.1 gene for waterlogging tolerance and early flowering, respectively, in cucumber (Cucumis sativus), and the ABA1/ZEP gene for thermotolerance in lettuce (Lactuca sativa) were efficiently identified (Lu et al, 2014;Huo et al, 2016;Xu et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes: MdSAUR37, MdPP2CH and MdALMTII

et al. 2018

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Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, using MapQTL and BSA-seq (bulk segregant analysis using next generation sequencing) with two independent pedigree-based populations, we identified four major genome-wide QTLs responsible for apple fruit acidity. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single-nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37 and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on the MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the fundamental physiological basis of quantitative genetics.

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“…BSA overcomes the constraints of near-isogenic lines and saves time and effort; it is widely used in marker development and gene mapping [16]. Because BSA does not require a large population, it is very popular in the study of the plant architecture traits of woody plants, such as apple (vertical traits) and peach (columnar and vertical traits) and in the development of genes and markers for peach weeping traits [2,10,50]. In ground-cover chrysanthemum, a random amplified polymorphic DNA (RAPD) marker A-10555 linked to the creeping trait was 7.96 cM from the loci controlling creeping/standard traits [51].…”

Section: Discussionmentioning

confidence: 99%

“…The genetic regulation of plant architecture traits in woody plants is more complex than in herbaceous plants and plant architecture traits are susceptible to external environmental conditions [5]. Many studies have been performed on plant architecture for extreme plant types of trees, including pillar and weeping peach [6], dwarf and compact peach (Prunus persica L.) [7], weeping Prunus mume [8], weeping Cercis chinensis [9], and columnar and weeping apple (Malus × domestica) [10,11].…”

Section: Introductionmentioning

confidence: 99%

Screening of Applicable SSR Molecular Markers Linked to Creeping Trait in Crape Myrtle

Zheng

Qin

et al. 2019

Forests

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Creeping plants have unique ornamental value because they have more branches and flowers and the creeping trait is rare in crape myrtle (Lagerstroemia indica L.). In this study, the first filial generation (F1) population was derived from Lagerstroemia fauriei Koehne (standard) and L. indica “Creole” (creeping) and the backcross1 (BC1) population was derived from the backcross of F1 individual S82 (creeping) and L. fauriei. The segregation of the creeping trait was analyzed for 174 seedlings of the BC1 population to examine the linkage relationship between simple sequence repeat (SSR) molecular markers and the creeping trait. Creeping genes were screened using bulked segregant analysis combined with 322 SSR primers, which were detected with good polymorphism. The results show that two SSR markers (S364 and LYS12) were detected, with genetic distances of 23.49 centimorgan (cM) and 25.86 cM from the loci controlling the plant opening angle trait and the branching angle trait, respectively. The accuracy rate for phenotypic verification using S364 and LYS12 was 76.51% and 74.14%, respectively. Our results provide basic information for the molecular marker-assisted selective breeding and cloning of the creeping gene to improve architecture diversity in the breeding of crape myrtle.

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Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus

Abstract: Identifying and exploiting three informative DNA variant segregation types in pooled genome sequencing analysis of the weeping phenotype in Malus empowers an effective genetic mapping strategy in out-crossing woody species.

Cited by 32 publications

References 74 publications

Loss of a highly conserved sterile alpha motif domain gene ( WEEP ) results in pendulous branch growth in peach trees

Loss of a highly conserved sterile alpha motif domain gene ( WEEP ) results in pendulous branch growth in peach trees

Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes: MdSAUR37, MdPP2CH and MdALMTII

Screening of Applicable SSR Molecular Markers Linked to Creeping Trait in Crape Myrtle

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