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Gabay G, Flaishman MA. Genetic and molecular regulation of chilling requirements in pear: breeding for climate change resilience. FRONTIERS IN PLANT SCIENCE 2024; 15:1347527. [PMID: 38736438 PMCID: PMC11082341 DOI: 10.3389/fpls.2024.1347527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/09/2024] [Indexed: 05/14/2024]
Abstract
Pear (Pyrus spp.) is a deciduous fruit tree that requires exposure to sufficient chilling hours during the winter to establish dormancy, followed by favorable heat conditions during the spring for normal vegetative and floral budbreak. In contrast to most temperate woody species, apples and pears of the Rosaceae family are insensitive to photoperiod, and low temperature is the major factor that induces growth cessation and dormancy. Most European pear (Pyrus Communis L.) cultivars need to be grown in regions with high chilling unit (CU) accumulation to ensure early vegetative budbreak. Adequate vegetative budbreak time will ensure suitable metabolite accumulation, such as sugars, to support fruit set and vegetative development, providing the necessary metabolites for optimal fruit set and development. Many regions that were suitable for pear production suffer from a reduction in CU accumulation. According to climate prediction models, many temperate regions currently suitable for pear cultivation will experience a similar accumulation of CUs as observed in Mediterranean regions. Consequently, the Mediterranean region can serve as a suitable location for conducting pear breeding trials aimed at developing cultivars that will thrive in temperate regions in the decades to come. Due to recent climatic changes, bud dormancy attracts more attention, and several studies have been carried out aiming to discover the genetic and physiological factors associated with dormancy in deciduous fruit trees, including pears, along with their related biosynthetic pathways. In this review, current knowledge of the genetic mechanisms associated with bud dormancy in European pear and other Pyrus species is summarized, along with metabolites and physiological factors affecting dormancy establishment and release and chilling requirement determination. The genetic and physiological insights gained into the factors regulating pear dormancy phase transition and determining chilling requirements can accelerate the development of new pear cultivars better suited to both current and predicted future climatic conditions.
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Affiliation(s)
- Gilad Gabay
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boker, Israel
| | - Moshe A. Flaishman
- Institute of Plant Sciences, Volcani Research Center, Rishon Lezion, Israel
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2
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Kumar A, Mushtaq M, Kumar P, Sharma DP, Gahlaut V. Insights into flowering mechanisms in apple (Malus × domestica Borkh.) amidst climate change: An exploration of genetic and epigenetic factors. Biochim Biophys Acta Gen Subj 2024; 1868:130593. [PMID: 38408683 DOI: 10.1016/j.bbagen.2024.130593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/05/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
Apple (Malus × domestica Borkh.) holds a prominent position among global temperate fruit crops, with flowering playing a crucial role in both production and breeding. This review delves into the intricate mechanisms governing apple flowering amidst the backdrop of climate change, acknowledging the profound influence of external and internal factors on biennial bearing, flower bud quality, and ultimately, fruit quality. Notably, the challenge faced in major apple production regions is not an inadequacy of flowers but an excess, leading to compromised fruit quality necessitating thinning practices. Climate change exacerbates these challenges, rendering apple trees more susceptible to crop failure due to unusual weather events, such as reduced winter snowfall, early spring cold weather, and hailstorms during flowering and fruit setting. Altered climatic conditions, exemplified by increased spring warming coupled with sub-freezing temperatures, negatively impact developing flower buds and decrease overall crop production. Furthermore, changing winter conditions affect chilling accumulation, disrupting flower development and synchronicity. Although the physiological perception of apple flowering has been reviewed in the past, the genetic, epigenetic, and multi-omics regulatory mechanisms governing floral induction and flowering are still rarely discussed in the case of apple flowering. This article comprehensively reviews the latest literature encompassing all aspects of apple flowering, aiming to broaden our understanding and address flowering challenges while also laying a solid foundation for future research in developing cultivars that are ideally adapted to climate change.
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Affiliation(s)
- Anshul Kumar
- MS Swaminathan School of Agriculture, Shoolini University, Bhajol, Solan, Himachal Pradesh 173229, India
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University, Bhajol, Solan, Himachal Pradesh 173229, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. YS Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh 173230, India.
| | - Dharam Paul Sharma
- Department of Fruit Science, Dr. YS Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh 173230, India
| | - Vijay Gahlaut
- University Centre for Research & Development, Chandigarh University, Punjab 140413, India.
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Puertes A, Polat H, Ramón-Núñez LA, González M, Ancillo G, Zuriaga E, Ríos G. Single-Bud Expression Analysis of Bud Dormancy Factors in Peach. PLANTS (BASEL, SWITZERLAND) 2023; 12:2601. [PMID: 37514216 PMCID: PMC10385799 DOI: 10.3390/plants12142601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
Transcriptomic and gene expression analysis have greatly facilitated the identification and characterization of transcriptional regulatory factors and effectors involved in dormancy progression and other physiological processes orchestrated during bud development in peach and other temperate fruit species. Gene expression measurements are most usually based on average values from several or many individual buds. We have performed single-bud gene analysis in flower buds of peach across dormancy release using amplicons from the master regulatory DORMANCY-ASSOCIATED MADS-BOX (DAM) factors, several jasmonic acid biosynthetic genes, other genes related to flowering development, cell growth resumption, and abiotic stress tolerance. This analysis provides a close view on gene-specific, single-bud variability throughout the developmental shift from dormant to dormancy-released stages, contributing to the characterization of putative co-expression modules and other regulatory aspects in this particular tissue.
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Affiliation(s)
- Ana Puertes
- Valencian Institute for Agricultural Research (IVIA), 46113 Valencia, Spain
| | - Helin Polat
- Valencian Institute for Agricultural Research (IVIA), 46113 Valencia, Spain
| | | | - Matilde González
- Valencian Institute for Agricultural Research (IVIA), 46113 Valencia, Spain
| | - Gema Ancillo
- Valencian Institute for Agricultural Research (IVIA), 46113 Valencia, Spain
| | - Elena Zuriaga
- Valencian Institute for Agricultural Research (IVIA), 46113 Valencia, Spain
| | - Gabino Ríos
- Valencian Institute for Agricultural Research (IVIA), 46113 Valencia, Spain
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Mignard P, Font i Forcada C, Giménez R, Moreno MÁ. Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm. PLANTS (BASEL, SWITZERLAND) 2023; 12:1249. [PMID: 36986937 PMCID: PMC10057825 DOI: 10.3390/plants12061249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
A basic knowledge of linkage disequilibrium and population structure is necessary in order to determine the genetic control and identify significant associations with agronomical and phytochemical compounds in apple (Malus × domestica Borkh). In this study, 186 apple accessions (Pop1), representing both Spanish native accessions (94) and non-Spanish cultivars (92) from the EEAD-CSIC apple core collection, were assessed using 23 SSRs markers. Four populations were considered: Pop1, Pop2, Pop3, and Pop4. The initial Pop1 was divided into 150 diploid (Pop2) and 36 triploid accessions (Pop3), while for the inter-chromosomal linkage disequilibrium and the association mapping analysis, 118 phenotype diploid accessions were considered Pop4. Thus, the average number of alleles per locus and observed heterozygosity for the overall sample set (Pop1) were 15.65 and 0.75, respectively. The population structure analysis identified two subpopulations in the diploid accessions (Pop2 and Pop4) and four in the triploids (Pop3). Regarding the Pop4, the population structure with K = 2 subpopulations segregation was in agreement with the UPGMA cluster analysis according to the genetic pairwise distances. Moreover, the accessions seemed to be segregated by their origin (Spanish/non-Spanish) in the clustering analysis. One of the two subpopulations encountered was quite-exclusively formed by non-Spanish accessions (30 out of 33). Furthermore, agronomical and basic fruit quality parameters, antioxidant traits, individual sugars, and organic acids were assessed for the association mapping analysis. A high level of biodiversity was exhibited in the phenotypic characterization of Pop4, and a total of 126 significant associations were found between the 23 SSR markers and the 21 phenotypic traits evaluated. This study also identified many new marker-locus trait associations for the first time, such as in the antioxidant traits or in sugars and organic acids, which may be useful for predictions and for a better understanding of the apple genome.
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Lempe J, Peil A, Flachowsky H. Time-Resolved Analysis of Candidate Gene Expression and Ambient Temperature During Bud Dormancy in Apple. FRONTIERS IN PLANT SCIENCE 2022; 12:803341. [PMID: 35111181 PMCID: PMC8802299 DOI: 10.3389/fpls.2021.803341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Winter dormancy - a period of low metabolic activity and no visible growth - appears as an adaptation to harsh winter conditions and can be divided into different phases. It is tightly controlled by environmental cues, with ambient temperature playing a major role. During endodormancy, a cultivar-specific amount of cold needs to be perceived, and during ecodormancy, heat hours accumulate before bud burst and anthesis in spring. Expression analysis, performed in several key fruit tree species, proved to be very useful in elucidating the molecular control of onset and release of dormancy. However, the time resolution of these experiments has been limited. Therefore, in this study, dense time-series expression analysis was conducted for 40 candidate genes involved in dormancy control, under the cool-temperate climate conditions in Dresden. Samples were taken from the cultivars 'Pinova' and 'Gala,' which differ in flowering time. The set of candidate genes included well-established dormancy genes such as DAM genes, MdFLC-like, MdICE1, MdPRE 1, and MdPIF4. Furthermore, we tested genes from dormancy-associated pathways including the brassinosteroid, gibberellic acid, abscisic acid (ABA), cytokinin response, and respiratory stress pathways. The expression patterns of well-established dormancy genes were confirmed and could be associated with specific dormancy phases. In addition, less well-known transcription factors and genes of the ABA signaling pathway showed associations with dormancy progression. The three ABA signaling genes HAB1_chr15, HAI3, and ABF2 showed a local minimum of gene expression in proximity of the endodormancy to ecodormancy transition. The number of sampling points allowed us to correlate expression values with temperature data, which revealed significant correlations of ambient temperature with the expression of the Malus domestica genes MdICE1, MdPIF4, MdFLC-like, HAB1chr15, and the type-B cytokinin response regulator BRR9. Interestingly, the slope of the linear correlation of temperature with the expression of MdPIF4 differed between cultivars. Whether the strength of inducibility of MdPIF4 expression by low temperature differs between the 'Pinova' and 'Gala' alleles needs to be tested further.
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Nishiyama S, Matsushita MC, Yamane H, Honda C, Okada K, Tamada Y, Moriya S, Tao R. Functional and expressional analyses of apple FLC-like in relation to dormancy progress and flower bud development. TREE PHYSIOLOGY 2021; 41:562-570. [PMID: 31728534 DOI: 10.1093/treephys/tpz111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/22/2019] [Indexed: 05/26/2023]
Abstract
We previously identified the FLOWERING LOCUS C (FLC)-like gene, a MADS-box transcription factor gene that belongs to Arabidopsis thaliana L. FLC clade, in apple (Malus $\times$ domestica Borkh.), and its expression in dormant flower buds is positively correlated with cumulative cold exposure. To elucidate the role of the MdFLC-like in the dormancy process and flower development, we first characterized the phenotypes of MdFLC-like overexpressing lines with the Arabidopsis Columbia-0 background. The overexpression of MdFLC-like significantly delayed the bolting date and reduced the plant size, but it did not significantly affect the number of rosette leaves or flower organ formation. Thus, MdFLC-like may affect vegetative growth and development rather than flowering when expressed in Arabidopsis, which is not like Arabidopsis FLC that affects development of flowering. We compared seasonal expression patterns of MdFLC-like in low-chill 'Anna' and high-chill 'Fuji' and 'Tsugaru' apples collected from trees grown in a cold winter region in temperate zone and found an earlier upregulation in 'Anna' compared with 'Fuji' and 'Tsugaru'. Expression patterns were also compared in relation to developmental changes in the flower primordia during the chilling accumulation period. Overall, MdFLC-like was progressively upregulated during flower primordia differentiation and development in autumn to early winter and reached a maximum expression level at around the same time as the genotype-dependent chilling requirements were fulfilled in high-chill cultivars. Thus, we hypothesize MdFLC-like may be upregulated in response to cold exposure and flower primordia development during the progress of endodormancy. Our study also suggests MdFLC-like may have a growth-inhibiting function during the end of endodormancy and ecodormancy when the temperature is low and unfavorable for rapid bud outgrowth.
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Affiliation(s)
- Soichiro Nishiyama
- Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | | | - Hisayo Yamane
- Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Chikako Honda
- Graduate School of Agricultural and Life Science, The University of Tokyo, Midori-Cho, Nishitokyo, Tokyo 188-0002, Japan
| | - Kazuma Okada
- Apple Research Station, Institute of Fruit Tree and Tea Science, NARO, Morioka 020-0123, Japan
| | - Yosuke Tamada
- National Institute for Basic Biology, Okazaki 444-8585, Japan
- School of Life Science, Sokendai, Okazaki 444-8585, Japan
| | - Shigeki Moriya
- Apple Research Station, Institute of Fruit Tree and Tea Science, NARO, Morioka 020-0123, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
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7
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Goeckeritz C, Hollender CA. There is more to flowering than those DAM genes: the biology behind bloom in rosaceous fruit trees. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101995. [PMID: 33444911 DOI: 10.1016/j.pbi.2020.101995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 05/06/2023]
Abstract
The regulation of bloom time in deciduous fruit trees is an area of increasing interest due to the negative impact of climate change on fruit production. Although flower development has been well-studied in model species, there are many knowledge gaps about this process in perennial fruit trees, whose floral development spans the four seasons and includes many temperature-driven transitions. To develop solutions for minimizing crop loss, a comprehensive research strategy is needed to understand flower development and bloom time in deciduous fruit trees. This approach must incorporate genetic, physiological, and phenological strategies which include morphological and molecular analyses. Here, we describe key floral development events for rosaceae family fruit trees, highlight recent molecular and genetic discoveries, and discuss future directions for this field.
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Affiliation(s)
- Charity Goeckeritz
- Michigan State University Department of Horticulture, East Lansing, MI 48824, United States
| | - Courtney A Hollender
- Michigan State University Department of Horticulture, East Lansing, MI 48824, United States.
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Zhang M, Yang Q, Yuan X, Yan X, Wang J, Cheng T, Zhang Q. Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume. FRONTIERS IN PLANT SCIENCE 2021; 12:690841. [PMID: 34335659 PMCID: PMC8319914 DOI: 10.3389/fpls.2021.690841] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/28/2021] [Indexed: 05/12/2023]
Abstract
Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests, and identified 1,445 candidate genes that are consistently linked with flowering time across multiple years. Furthermore, we assessed the global transcriptome change of floral buds from the two P. mume cultivars exhibiting contrasting bloom dates and detected 617 associated genes that were differentially expressed during the flowering process. By integrating a co-expression network analysis, we screened out 191 gene candidates of conserved transcriptional pattern during blooming across cultivars. Finally, we validated the temporal expression profiles of these candidates and highlighted their putative roles in regulating floral bud break and blooming time in P. mume. Our findings are important to expand the understanding of flowering time control in woody perennials and will boost the molecular breeding of novel varieties in P. mume.
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Affiliation(s)
- Man Zhang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qingqing Yang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xi Yuan
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | | | - Jia Wang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- National Engineering Research Center for Floriculture, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- *Correspondence: Qixiang Zhang
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Guo X, Khare S, Silvestro R, Huang J, Sylvain JD, Delagrange S, Rossi S. Minimum spring temperatures at the provenance origin drive leaf phenology in sugar maple populations. TREE PHYSIOLOGY 2020; 40:1639-1647. [PMID: 32705120 DOI: 10.1093/treephys/tpaa096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/28/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Late frost can cause damage to trees, especially to the developing bud of broadleaf species in spring. Through long-term adaptation, plants adjust leaf phenology to achieve an optimal trade-off between growing season length and frost avoidance. In this study, we aim to assess ecotypic differentiation in leaf development of sugar maple populations planted in a common garden. A total of 272 sugar maple seedlings from 29 Canadian provenances were planted at the northern boundary of the natural range, and the phenological phases of bud and leaf development were monitored during spring 2019. The wide geographical area under evaluation showed a complex seasonal pattern of temperature, with spring warming occurring later in the north and close to the sea. Overall, leaf development lasted between 20 and 36 days, from the end of May to end of June. We observed different timings and rates of leaf development among provenances, demonstrating the occurrence of ecotypes in this species. Minimum April temperatures of the original sites were able to explain such differences, while maximum April temperatures were not significant. Seedlings from sites with colder minimum April temperatures completed leaf development earlier and faster. On average, leaf development diverged by up to 6 days among provenances, with minimum April temperatures ranging from -3 to 3 °C. Our results demonstrated that the avoidance of late spring frost is a driving force of leaf development in sugar maple populations. In the colder sites, the growing season is a limiting factor for tree growth. Thus, when thermal conditions become favorable in spring, an earlier growth reactivation and high metabolic activity ensure a fast leaf emission, which maximizes the period available for photosynthesis and growth. These patterns demonstrate the long-term phenological adaptation of sugar maple populations to local climatic conditions and suggest the importance of frost events for leaf development.
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Affiliation(s)
- Xiali Guo
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
- Center of Plant Ecology, Core Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
- Département des Sciences Fondamentales, Université du Quebec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi, QC G7H 2B1,Canada
| | - Siddhartha Khare
- Département des Sciences Fondamentales, Université du Quebec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi, QC G7H 2B1,Canada
| | - Roberto Silvestro
- Département des Sciences Fondamentales, Université du Quebec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi, QC G7H 2B1,Canada
| | - Jianguo Huang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
- Center of Plant Ecology, Core Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Jean-Daniel Sylvain
- Direction de la Recherche Forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 rue Einstein, Québec, QC G1P 3W8, Canada
| | - Sylvain Delagrange
- Department of Natural Sciences, University of Quebec in Outaouais (UQO), 58 Main Street, Ripon, QC J0V 1W0, Canada
| | - Sergio Rossi
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
- Département des Sciences Fondamentales, Université du Quebec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi, QC G7H 2B1,Canada
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10
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Jung M, Roth M, Aranzana MJ, Auwerkerken A, Bink M, Denancé C, Dujak C, Durel CE, Font I Forcada C, Cantin CM, Guerra W, Howard NP, Keller B, Lewandowski M, Ordidge M, Rymenants M, Sanin N, Studer B, Zurawicz E, Laurens F, Patocchi A, Muranty H. The apple REFPOP-a reference population for genomics-assisted breeding in apple. HORTICULTURE RESEARCH 2020; 7:189. [PMID: 33328447 PMCID: PMC7603508 DOI: 10.1038/s41438-020-00408-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/25/2020] [Accepted: 09/06/2020] [Indexed: 05/16/2023]
Abstract
Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker-trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker-trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.
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Affiliation(s)
- Michaela Jung
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Morgane Roth
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
- GAFL, INRAE, 84140, Montfavet, France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | | | - Marco Bink
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Hendrix Genetics Research, Technology and Services B.V., PO Box 114, 5830AC, Boxmeer, The Netherlands
| | - Caroline Denancé
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Charles-Eric Durel
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Carolina Font I Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Celia M Cantin
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- ARAID (Fundación Aragonesa para la Investigación y el Desarrollo), 50018, Zaragoza, Spain
| | | | - Nicholas P Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
- Institute of Biology and Environmental Sciences, University of Oldenburg, 26129, Oldenburg, Germany
| | - Beat Keller
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | | | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, RG6 6AR, Reading, UK
| | - Marijn Rymenants
- Better3fruit N.V., 3202, Rillaar, Belgium
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001, Leuven, Belgium
| | - Nadia Sanin
- Research Centre Laimburg, 39040, Auer, Italy
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Edward Zurawicz
- Research Institute of Horticulture, 96-100, Skierniewice, Poland
| | - François Laurens
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Andrea Patocchi
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Hélène Muranty
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France.
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11
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Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. Apple whole genome sequences: recent advances and new prospects. HORTICULTURE RESEARCH 2019; 6:59. [PMID: 30962944 PMCID: PMC6450873 DOI: 10.1038/s41438-019-0141-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 05/19/2023]
Abstract
In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
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Affiliation(s)
- Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Luca Bianco
- Computational Biology, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Nicholas P. Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108 USA
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Amandine Cornille
- GQE – Le Moulon, Institut National de la Recherche Agronomique, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charles-Eric Durel
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Ltd, Motueka, 7198 New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Evelyne Costes
- AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Gennaro Fazio
- Plant Genetic Resources Unit, USDA ARS, Geneva, NY 14456 USA
| | - Hisayo Yamane
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chris Gottschalk
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, 100193 Beijing, China
| | | | - Susan E. Gardiner
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Craig Hardner
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, 4072 Australia
| | - Satish Kumar
- New Cultivar Innovation, Plant and Food Research, Havelock North, 4130 New Zealand
| | - Francois Laurens
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Etienne Bucher
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
- Agroscope, 1260 Changins, Switzerland
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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12
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Miotto YE, Tessele C, Czermainski ABC, Porto DD, Falavigna VDS, Sartor T, Cattani AM, Delatorre CA, de Alencar SA, da Silva-Junior OB, Togawa RC, Costa MMDC, Pappas GJ, Grynberg P, de Oliveira PRD, Kvitschal MV, Denardi F, Buffon V, Revers LF. Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Genes From the Cold Perception Pathway to Dormancy Release in Apple ( Malus × domestica Borkh.). FRONTIERS IN PLANT SCIENCE 2019; 10:33. [PMID: 30930909 PMCID: PMC6423911 DOI: 10.3389/fpls.2019.00033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/10/2019] [Indexed: 05/26/2023]
Abstract
Chilling requirement (CR) for bud dormancy completion determines the time of bud break in apple (Malus × domestica Borkh.). The molecular control of bud dormancy is highly heritable, suggesting a strong genetic control of the trait. An available Infinium II SNP platform for genotyping containing 8,788 single nucleotide polymorphic markers was employed, and linkage maps were constructed in a F1 cross from the low CR M13/91 and the moderate CR cv. Fred Hough. These maps were used to identify quantitative trait loci (QTL) for bud break date as a trait related to dormancy release. A major QTL for bud break was detected at the beginning of linkage group 9 (LG9). This QTL remained stable during seven seasons in two different growing sites. To increase mapping efficiency in detecting contributing genes underlying this QTL, 182 additional SNP markers located at the locus for bud break were used. Combining linkage mapping and structural characterization of the region, the high proportion of the phenotypic variance in the trait explained by the QTL is related to the coincident positioning of Arabidopsis orthologs for ICE1, FLC, and PRE1 protein-coding genes. The proximity of these genes from the most explanatory markers of this QTL for bud break suggests potential genetic additive effects, reinforcing the hypothesis of inter-dependent mechanisms controlling dormancy induction and release in apple trees.
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Affiliation(s)
- Yohanna Evelyn Miotto
- Department of Crop Science, Agronomy School, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Carolina Tessele
- Department of Crop Science, Agronomy School, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Vítor da Silveira Falavigna
- Embrapa Uva e Vinho, Bento Gonçalves, Brazil
- Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Tiago Sartor
- Embrapa Uva e Vinho, Bento Gonçalves, Brazil
- Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Amanda Malvessi Cattani
- Embrapa Uva e Vinho, Bento Gonçalves, Brazil
- Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Carla Andrea Delatorre
- Department of Crop Science, Agronomy School, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Sérgio Amorim de Alencar
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | | | | | | | | | | | | | - Marcus Vinícius Kvitschal
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina – Epagri – Estação Experimental de Caçador, Caçador, Brazil
| | - Frederico Denardi
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina – Epagri – Estação Experimental de Caçador, Caçador, Brazil
| | | | - Luís Fernando Revers
- Embrapa Uva e Vinho, Bento Gonçalves, Brazil
- Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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13
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Gabay G, Faigenboim A, Dahan Y, Izhaki Y, Itkin M, Malitsky S, Elkind Y, Flaishman MA. Transcriptome analysis and metabolic profiling reveal the key role of α-linolenic acid in dormancy regulation of European pear. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1017-1031. [PMID: 30590791 PMCID: PMC6363095 DOI: 10.1093/jxb/ery405] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/17/2018] [Indexed: 05/22/2023]
Abstract
Deciduous trees require sufficient chilling during winter dormancy to grow. To decipher the dormancy-regulating mechanism, we carried out RNA sequencing (RNA-Seq) analysis and metabolic profiling of European pear (Pyrus communis L.) vegetative buds during the dormancy phases. Samples were collected from two cultivars that differed greatly in their chilling requirements: 'Spadona' (SPD), a low chilling requirement cultivar; and Harrow Sweet (HS), a high chilling requirement cultivar. Comparative transcriptome analysis revealed >8500 differentially expressed transcripts; most were related to metabolic pathways. Out of 174 metabolites, 44 displayed differential levels in both cultivars, 38 were significantly changed only in SPD, and 15 only in HS. Phospholipids were mostly accumulated at the beginning of dormancy, sugars between before dormancy and mid-dormancy, and fatty acids, including α-linolenic acid, at dormancy break. Differentially expressed genes underlying previously identified major quantitative trait loci (QTLs) in linkage group 8 included genes related to the α-linolenic acid pathway, 12-oxophytodienoate reductase 2-like, and the DORMANCY-ASSOCIATED MADS-BOX (DAM) genes, PcDAM1 and PcDAM2, putative orthologs of PpDAM1 and PpDAM2, confirming their role for the first time in European pear. Additional new putative dormancy-related uncharacterized genes and genes related to metabolic pathways are suggested. These results suggest the crucial role of α-linolenic acid and DAM genes in pear bud dormancy phase transitions.
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Affiliation(s)
- Gilad Gabay
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim, Rishon Lezion, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Adi Faigenboim
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim, Rishon Lezion, Israel
| | - Yardena Dahan
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim, Rishon Lezion, Israel
| | - Yacov Izhaki
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim, Rishon Lezion, Israel
| | - Maxim Itkin
- Life Science Core Facilities, Weitzman Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Life Science Core Facilities, Weitzman Institute of Science, Rehovot, Israel
| | - Yonatan Elkind
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Moshe A Flaishman
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim, Rishon Lezion, Israel
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14
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Gabay G, Dahan Y, Izhaki Y, Faigenboim A, Ben-Ari G, Elkind Y, Flaishman MA. High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time. BMC PLANT BIOLOGY 2018; 18:175. [PMID: 30165824 PMCID: PMC6117884 DOI: 10.1186/s12870-018-1386-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 08/07/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Genomic analysis technologies can promote efficient fruit tree breeding. Genotyping by sequencing (GBS) enables generating efficient data for high-quality genetic map construction and QTL analysis in a relatively accessible way. Furthermore, High-resolution genetic map construction and accurate QTL detection can significantly narrow down the putative candidate genes associated with important plant traits. RESULTS We genotyped 162 offspring in the F1 'Spadona' x 'Harrow Sweet' pear population using GBS. An additional 21 pear accessions, including the F1 population's parents, from our germplasm collection were subjected to GBS to examine diverse genetic backgrounds that are associated to agriculturally relevant traits and to enhance the power of SNP calling. A standard SNP calling pipeline identified 206,971 SNPs with Asian pear ('Suli') as the reference genome and 148,622 SNPs with the European genome ('Bartlett'). These results enabled constructing a genetic map, after further stringent SNP filtering, consisting of 2036 markers on 17 linkage groups with a length of 1433 cM and an average marker interval of 0.7 cM. We aligned 1030 scaffolds covering a total size of 165.5 Mbp (29%) of the European pear genome to the 17 linkage groups. For high-resolution QTL analysis covering the whole genome, we used phenotyping for vegetative budbreak time in the F1 population. New QTLs associated to vegetative budbreak time were detected on linkage groups 5, 13 and 15. A major QTL on linkage group 8 and an additional QTL on linkage group 9 were confirmed. Due to the significant genotype-by-environment (GxE) effect, we were able to identify novel interaction QTLs on linkage groups 5, 8, 9 and 17. Phenotype-genotype association analysis in the pear accessions for main genotype effect was conducted to support the QTLs detected in the F1 population. Significant markers were detected on every linkage group to which main genotype effect QTLs were mapped. CONCLUSIONS This is the first vegetative budbreak study of European pear that makes use of high-resolution genetic mapping. These results provide tools for marker-assisted selection and accurate QTL analysis in pear, and specifically at vegetative budbreak, considering the significant GxE and phenotype-plasticity effects.
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Affiliation(s)
- Gilad Gabay
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, Rishon Lezion, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, P.O. Box 12, 76100, Rehovot, Israel
| | - Yardena Dahan
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, Rishon Lezion, Israel
| | - Yacov Izhaki
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, Rishon Lezion, Israel
| | - Adi Faigenboim
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, Rishon Lezion, Israel
| | - Giora Ben-Ari
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, Rishon Lezion, Israel
| | - Yonatan Elkind
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, P.O. Box 12, 76100, Rehovot, Israel
| | - Moshe A Flaishman
- Institute of Plant Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, Rishon Lezion, Israel.
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15
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Laurens F, Aranzana MJ, Arus P, Bassi D, Bink M, Bonany J, Caprera A, Corelli-Grappadelli L, Costes E, Durel CE, Mauroux JB, Muranty H, Nazzicari N, Pascal T, Patocchi A, Peil A, Quilot-Turion B, Rossini L, Stella A, Troggio M, Velasco R, van de Weg E. An integrated approach for increasing breeding efficiency in apple and peach in Europe. HORTICULTURE RESEARCH 2018; 5:11. [PMID: 29507735 PMCID: PMC5830435 DOI: 10.1038/s41438-018-0016-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/23/2017] [Indexed: 05/02/2023]
Abstract
Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.
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Affiliation(s)
- Francois Laurens
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona Spain
| | - Pere Arus
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona Spain
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan, 20133 Italy
| | - Marco Bink
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708PB The Netherlands
- Present Address: Hendrix Genetics Research, Technology & Services, Boxmeer, 5830 AC The Netherlands
| | - Joan Bonany
- IRTA-Mas Badia, Mas Badia, La Tallada, 17134 Spain
| | - Andrea Caprera
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | | | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | | | - Hélène Muranty
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | - Nelson Nazzicari
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | - Andrea Patocchi
- Agroscope, Research Division Plant Breeding, Schloss 1, Wädenswil, 8820 Switzerland
| | - Andreas Peil
- Julius Kühn-Institute (JKI); Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, Dresden, 01326 Germany
| | | | - Laura Rossini
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan, 20133 Italy
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Alessandra Stella
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Riccardo Velasco
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- CREA-VE, Center of Viticulture and Enology, via XXVIII Aprile 26, Conegliano (TV), 31015 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O.Box 386, Wageningen, 6700AJ The Netherlands
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16
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Falavigna VDS, Guitton B, Costes E, Andrés F. I Want to (Bud) Break Free: The Potential Role of DAM and SVP-Like Genes in Regulating Dormancy Cycle in Temperate Fruit Trees. FRONTIERS IN PLANT SCIENCE 2018; 9:1990. [PMID: 30687377 PMCID: PMC6335348 DOI: 10.3389/fpls.2018.01990] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 12/20/2018] [Indexed: 05/18/2023]
Abstract
Bud dormancy is an adaptive process that allows trees to survive the hard environmental conditions that they experience during the winter of temperate climates. Dormancy is characterized by the reduction in meristematic activity and the absence of visible growth. A prolonged exposure to cold temperatures is required to allow the bud resuming growth in response to warm temperatures. In fruit tree species, the dormancy cycle is believed to be regulated by a group of genes encoding MADS-box transcription factors. These genes are called DORMANCY-ASSOCIATED MADS-BOX (DAM) and are phylogenetically related to the Arabidopsis thaliana floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS-LIKE 24. The interest in DAM and other orthologs of SVP (SVP-like) genes has notably increased due to the publication of several reports suggesting their role in the control of bud dormancy in numerous fruit species, including apple, pear, peach, Japanese apricot, and kiwifruit among others. In this review, we briefly describe the physiological bases of the dormancy cycle and how it is genetically regulated, with a particular emphasis on DAM and SVP-like genes. We also provide a detailed report of the most recent advances about the transcriptional regulation of these genes by seasonal cues, epigenetics and plant hormones. From this information, we propose a tentative classification of DAM and SVP-like genes based on their seasonal pattern of expression. Furthermore, we discuss the potential biological role of DAM and SVP-like genes in bud dormancy in antagonizing the function of FLOWERING LOCUS T-like genes. Finally, we draw a global picture of the possible role of DAM and SVP-like genes in the bud dormancy cycle and propose a model that integrates these genes in a molecular network of dormancy cycle regulation in temperate fruit trees.
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17
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Durand JB, Allard A, Guitton B, van de Weg E, Bink MCAM, Costes E. Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping. FRONTIERS IN PLANT SCIENCE 2017; 8:858. [PMID: 28638387 PMCID: PMC5461300 DOI: 10.3389/fpls.2017.00858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/08/2017] [Indexed: 05/18/2023]
Abstract
Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γ g ) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γ g and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on a posteriori sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species.
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Affiliation(s)
- Jean-Baptiste Durand
- Laboratoire Jean Kuntzmann, Inria Mistis, Université Grenoble AlpesGrenoble, France
- Virtual Plants Team, Inria and CIRAD, UMR AGAPMontpellier, France
| | - Alix Allard
- Equipe Architecture et Fonctionnement des Espèces Fruitières, UMR AGAP, Institut National de la Recherche AgronomiqueMontpellier, France
| | - Baptiste Guitton
- Equipe Architecture et Fonctionnement des Espèces Fruitières, UMR AGAP, Institut National de la Recherche AgronomiqueMontpellier, France
| | - Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University and ResearchWageningen, Netherlands
| | - Marco C. A. M. Bink
- Biometris, Wageningen University and ResearchWageningen, Netherlands
- Research & Technology Centre, Hendrix GeneticsBoxmeer, Netherlands
| | - Evelyne Costes
- Equipe Architecture et Fonctionnement des Espèces Fruitières, UMR AGAP, Institut National de la Recherche AgronomiqueMontpellier, France
- *Correspondence: Evelyne Costes
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Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton JM, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M, Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE. Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple. FRONTIERS IN PLANT SCIENCE 2017; 8:1923. [PMID: 29176988 PMCID: PMC5686452 DOI: 10.3389/fpls.2017.01923] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 05/17/2023]
Abstract
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
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Affiliation(s)
- Jorge Urrestarazu
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
- Department of Agricultural Sciences, Public University of Navarre, Pamplona, Spain
- *Correspondence: Jorge Urrestarazu
| | - Hélène Muranty
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Caroline Denancé
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Diane Leforestier
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Elisa Ravon
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Arnaud Guyader
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Rémi Guisnel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Laurence Feugey
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Sébastien Aubourg
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Marc Lateur
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Patrick Houben
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | | | - Jiri Sedlak
- Research and Breeding Institute of Pomology Holovousy Ltd., Horice, Czechia
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | | | | | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | - Charles Poncet
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Anthony Théron
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Shigeki Moriya
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Marco C. A. M. Bink
- Wageningen UR, Biometris, Wageningen, Netherlands
- Hendrix Genetics, Boxmeer, Netherlands
| | - François Laurens
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Charles-Eric Durel
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Sun MY, Fu XL, Tan QP, Liu L, Chen M, Zhu CY, Li L, Chen XD, Gao DS. Analysis of basic leucine zipper genes and their expression during bud dormancy in peach (Prunus persica). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 104:54-70. [PMID: 27107182 DOI: 10.1016/j.plaphy.2016.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 06/05/2023]
Abstract
Dormancy is a biological characteristic developed to resist the cold conditions in winter. The bZIP transcription factors are present exclusively in eukaryotes and have been identified and classified in many species. bZIP proteins are known to regulate numerous biological processes, however, the role of bZIP in bud dodormancy has not been studied extensively. In total, 50 PpbZIP transcription factor-encoding genes were identified and categorized them into 10 groups (A-I and S). Similar intron/exon structures, additional conserved motifs, and DNA-binding site specificity supported our classification scheme. Additionally, chromosomal distribution and collinearity analyses suggested that expansion of the PpbZIP transcription factor family was due to segment/chromosomal duplications. We also predicted the dimerization properties based on characteristic features of the leucine zipper and classified PpbZIP proteins into 23 subfamilies. Furthermore, qRT-PCR results indicated that PpbZIPs genes may be involved in regulating dormancy. The same gene of different species might participate in different regulating networks through interactions with specific partners. Our expression profiling results complemented the microarray data, suggesting that co-expression patterns of bZIP transcription factors during dormancy differed among deciduous fruit trees. Our findings further clarify the molecular characteristics of the PpbZIP transcription factor family, including potential gene functions during dormancy. This information may facilitate further research on the evolutionary history and biological functions of bZIP proteins in peach and other rosaceae plants.
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Affiliation(s)
- Ming-Yue Sun
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Xi-Ling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Qiu-Ping Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Li Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Min Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Cui-Ying Zhu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Xiu-De Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Dong-Sheng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China.
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Anh Tuan P, Bai S, Saito T, Imai T, Ito A, Moriguchi T. Involvement of EARLY BUD-BREAK, an AP2/ERF Transcription Factor Gene, in Bud Break in Japanese Pear (Pyrus pyrifolia Nakai) Lateral Flower Buds: Expression, Histone Modifications and Possible Target Genes. PLANT & CELL PHYSIOLOGY 2016; 57:1038-47. [PMID: 26940832 DOI: 10.1093/pcp/pcw041] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/19/2016] [Indexed: 05/05/2023]
Abstract
In the Japanese pear (Pyrus pyrifolia Nakai) 'Kosui', three developmental stages of lateral flower buds have been proposed to occur during ecodormancy to the flowering phase, i.e. rapid enlargement, sprouting and flowering. Here, we report an APETALA2/ethylene-responsive factor (AP2/ERF) transcription factor gene, named pear EARLY BUD-BREAK (PpEBB), which was highly expressed during the rapid enlargement stage occurring prior to the onset of bud break in flower buds. Gene expression analysis revealed that PpEBB expression was dramatically increased during the rapid enlargement stage in three successive growing seasons. PpEBB transcript levels peaked 1 week prior to onset of bud break in 'Kosui' potted plants treated with hydrogen cyanamide or water under forcing conditions. Chromatin immunoprecipitation-quantitative PCR showed that higher levels of active histone modifications (trimethylation of the histone H3 tail at Lys4) in the 5'-upstream and start codon regions of the PpEBB gene were associated with the induced expression level of PpEBB during the rapid enlargement stage. In addition, we provide evidence that PpEBB may interact with and regulate pear four D-type cyclin (PpCYCD3) genes during bud break in 'Kosui' lateral flower buds. PpEBB significantly increased the promoter activities of four PpCYCD3 genes in a dual-luciferase assay using tobacco leaves. Taken together, our findings uncovered aspects of the bud break regulatory mechanism in the Japanese pear and provided further evidence that the EBB family plays an important role in bud break in perennial plants.
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Affiliation(s)
- Pham Anh Tuan
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan
| | - Songling Bai
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan Present address: Institute of Fruit Science, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Takanori Saito
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan Present address: Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8510 Japan
| | - Tsuyoshi Imai
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan
| | - Akiko Ito
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan
| | - Takaya Moriguchi
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan
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21
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Mapping Temperate Vegetation Climate Adaptation Variability Using Normalized Land Surface Phenology. CLIMATE 2016. [DOI: 10.3390/cli4020024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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22
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Allard A, Bink MCAM, Martinez S, Kelner JJ, Legave JM, di Guardo M, Di Pierro EA, Laurens F, van de Weg EW, Costes E. Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2875-88. [PMID: 27034326 PMCID: PMC4861029 DOI: 10.1093/jxb/erw130] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6-21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase.
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Affiliation(s)
- Alix Allard
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro, F-34398 Montpellier, France Montpellier SupAgro, UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro, F-34398 Montpellier, France
| | - Marco C A M Bink
- Biometris, Wageningen University and Research centre, Droevendaalsesteeg 1, PO Box 16, 6700AA, Wageningen, The Netherlands
| | - Sébastien Martinez
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro, F-34398 Montpellier, France
| | - Jean-Jacques Kelner
- Montpellier SupAgro, UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro, F-34398 Montpellier, France
| | - Jean-Michel Legave
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro, F-34398 Montpellier, France
| | - Mario di Guardo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 16, 6700AA, Wageningen, The Netherlands
| | - Erica A Di Pierro
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - François Laurens
- INRA, UMR1345, Institut de Recherche en Horticulture et Semences IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QUASAV, F-49071 Beaucouzé, France
| | - Eric W van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 16, 6700AA, Wageningen, The Netherlands
| | - Evelyne Costes
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro, F-34398 Montpellier, France
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23
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Boocock J, Chagné D, Merriman TR, Black MA. The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh. BMC Genomics 2015; 16:848. [PMID: 26493398 PMCID: PMC4618995 DOI: 10.1186/s12864-015-2096-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/15/2015] [Indexed: 11/14/2022] Open
Abstract
Background Copy number variation (CNV) is a common feature of eukaryotic genomes, and a growing body of evidence suggests that genes affected by CNV are enriched in processes that are associated with environmental responses. Here we use next generation sequence (NGS) data to detect copy-number variable regions (CNVRs) within the Malus x domestica genome, as well as to examine their distribution and impact. Methods CNVRs were detected using NGS data derived from 30 accessions of M. x domestica analyzed using the read-depth method, as implemented in the CNVrd2 software. To improve the reliability of our results, we developed a quality control and analysis procedure that involved checking for organelle DNA, not repeat masking, and the determination of CNVR identity using a permutation testing procedure. Results Overall, we identified 876 CNVRs, which spanned 3.5 % of the apple genome. To verify that detected CNVRs were not artifacts, we analyzed the B- allele-frequencies (BAF) within a single nucleotide polymorphism (SNP) array dataset derived from a screening of 185 individual apple accessions and found the CNVRs were enriched for SNPs having aberrant BAFs (P < 1e-13, Fisher’s Exact test). Putative CNVRs overlapped 845 gene models and were enriched for resistance (R) gene models (P < 1e-22, Fisher’s exact test). Of note was a cluster of resistance gene models on chromosome 2 near a region containing multiple major gene loci conferring resistance to apple scab. Conclusion We present the first analysis and catalogue of CNVRs in the M. x domestica genome. The enrichment of the CNVRs with R gene models and their overlap with gene loci of agricultural significance draw attention to a form of unexplored genetic variation in apple. This research will underpin further investigation of the role that CNV plays within the apple genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2096-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Boocock
- Department of Biochemistry, University of Otago, Dunedin, New Zealand. .,The Virtual Institute of Statistical Genetics (VISG), Rotorua, New Zealand.
| | - David Chagné
- The Virtual Institute of Statistical Genetics (VISG), Rotorua, New Zealand.,The New Zealand Institute for Plant & Food Research Ltd, Palmerston North, New Zealand
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,The Virtual Institute of Statistical Genetics (VISG), Rotorua, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand. .,The Virtual Institute of Statistical Genetics (VISG), Rotorua, New Zealand.
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24
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Falginella L, Cipriani G, Monte C, Gregori R, Testolin R, Velasco R, Troggio M, Tartarini S. A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'. BMC PLANT BIOLOGY 2015; 15:150. [PMID: 26084469 PMCID: PMC4472412 DOI: 10.1186/s12870-015-0507-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/27/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Russeting is a disorder developed by apple fruits that consists of cuticle cracking followed by the replacement of the epidermis by a corky layer that protects the fruit surface from water loss and pathogens. Although influenced by many environmental conditions and orchard management practices, russeting is under genetic control. The difficulty in classifying offspring and consequent variable segregation ratios have led several authors to conclude that more than one genetic determinant could be involved, although some evidence favours a major gene (Ru). RESULTS In this study we report the mapping of a major genetic russeting determinant on linkage group 12 of apple as inferred from the phenotypic observation in a segregating progeny derived from 'Renetta Grigia di Torriana', the construction of a 20 K Illumina SNP chip based genetic map, and QTL analysis. Recombination analysis in two mapping populations restricted the region of interest to approximately 400 Kb. Of the 58 genes predicted from the Golden Delicious sequence, a putative ABCG family transporter has been identified. Within a small set of russeted cultivars tested with markers of the region, only six showed the same haplotype of 'Renetta Grigia di Torriana'. CONCLUSIONS A major determinant (Ru_RGT) for russeting development putatively involved in cuticle organization is proposed as a candidate for controlling the trait. SNP and SSR markers tightly co-segregating with the Ru_RGT locus may assist the breeder selection. The observed segregations and the analysis of the 'Renetta Grigia di Torriana' haplotypic region in a panel of russeted and non-russeted cultivars may suggest the presence of other determinants for russeting in apple.
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Affiliation(s)
- Luigi Falginella
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Guido Cipriani
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Corinne Monte
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Via Fanin 44, 40127, Bologna, Italy.
| | - Raffaele Testolin
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Riccardo Velasco
- Research and Innovation Centre - Fondazione Edmund Mach - Department of Genomics and Biology of Fruit Crop, Via E. Mach 1, 38010 S, Michele all'Adige TN, Italy.
| | - Michela Troggio
- Research and Innovation Centre - Fondazione Edmund Mach - Department of Genomics and Biology of Fruit Crop, Via E. Mach 1, 38010 S, Michele all'Adige TN, Italy.
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Via Fanin 44, 40127, Bologna, Italy.
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25
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Leforestier D, Ravon E, Muranty H, Cornille A, Lemaire C, Giraud T, Durel CE, Branca A. Genomic basis of the differences between cider and dessert apple varieties. Evol Appl 2015; 8:650-61. [PMID: 26240603 PMCID: PMC4516418 DOI: 10.1111/eva.12270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/15/2015] [Indexed: 12/26/2022] Open
Abstract
Unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. It can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. Apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. Sweet dessert apples are used for direct consumption, while bitter cider apples are used to produce cider. Several important traits are known to differentiate the two variety types, in particular fruit size, biennial versus annual fruit bearing, and bitterness, caused by a higher content in polyphenols. Here, we used an Illumina 8k SNP chip on two core collections, of 48 dessert and 48 cider apples, respectively, for identifying genomic regions responsible for the differences between cider and dessert apples. The genome-wide level of genetic differentiation between cider and dessert apples was low, although 17 candidate regions showed signatures of divergent selection, displaying either outlier FST values or significant association with phenotypic traits (bitter versus sweet fruits). These candidate regions encompassed 420 genes involved in a variety of functions and metabolic pathways, including several colocalizations with QTLs for polyphenol compounds.
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Affiliation(s)
- Diane Leforestier
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Elisa Ravon
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Hélène Muranty
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Christophe Lemaire
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Charles-Eric Durel
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
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Saito T, Tuan PA, Katsumi-Horigane A, Bai S, Ito A, Sekiyama Y, Ono H, Moriguchi T. Development of flower buds in the Japanese pear (Pyrus pyrifolia) from late autumn to early spring. TREE PHYSIOLOGY 2015; 35:653-62. [PMID: 26063707 DOI: 10.1093/treephys/tpv043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/09/2015] [Indexed: 05/03/2023]
Abstract
We periodically investigated the lateral flower bud morphology of 1-year shoots of 'Kosui' pears (Pyrus pyrifolia Nakai) in terms of dormancy progression, using magnetic resonance imaging. The size of flower buds did not change significantly during endodormancy, but rapid enlargement took place at the end of the ecodormancy stage. To gain insight into the physiological status during this period, we analyzed gene expression related to cell cycle-, cell expansion- and water channel-related genes, namely cyclin (CYC), expansin (EXPA), tonoplast intrinsic proteins (TIP) and plasma membrane intrinsic proteins (PIP). Constant but low expression of pear cyclin genes (PpCYCD3s) was observed in the transition phase from endodormancy to ecodormancy. The expression levels of PpCYCD3s were consistent with few changes in flower bud size, but up-regulated before the sprouting stage. In contrast, the expression of pear expansin and water channel-related genes (PpEXPA2, PpPIP2A, PpPIP2B, PpIδTIP1A and PpIδTIP1B) were low until onset of the rapid enlargement stage of flower buds. However, expression of these genes rapidly increased during sprouting along with a gradual increase of free water content in the floral primordia of buds. Taken together, these results suggest that flower bud size tends to stay constant until the endodormancy phase transition. Rapid enlargement of flower buds observed in March is partly due to the enhancement of the cell cycle. Then, sprouting takes place concomitant with the increase in cell expansion and free water movement.
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Affiliation(s)
- Takanori Saito
- NARO Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Pham Anh Tuan
- NARO Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Akemi Katsumi-Horigane
- National Food Research Institute, NARO, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Songling Bai
- NARO Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Akiko Ito
- NARO Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Yasuyo Sekiyama
- National Food Research Institute, NARO, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Hiroshi Ono
- National Food Research Institute, NARO, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Takaya Moriguchi
- NARO Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
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Porto DD, Bruneau M, Perini P, Anzanello R, Renou JP, dos Santos HP, Fialho FB, Revers LF. Transcription profiling of the chilling requirement for bud break in apples: a putative role for FLC-like genes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2659-72. [PMID: 25750421 DOI: 10.1093/jxb/erv061] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Apple production depends on the fulfilment of a chilling requirement for bud dormancy release. Insufficient winter chilling results in irregular and suboptimal bud break in the spring, with negative impacts on apple yield. Trees from apple cultivars with contrasting chilling requirements for bud break were used to investigate the expression of the entire set of apple genes in response to chilling accumulation in the field and controlled conditions. Total RNA was analysed on the AryANE v.1.0 oligonucleotide microarray chip representing 57,000 apple genes. The data were tested for functional enrichment, and differential expression was confirmed by real-time PCR. The largest number of differentially expressed genes was found in samples treated with cold temperatures. Cold exposure mostly repressed expression of transcripts related to photosynthesis, and long-term cold exposure repressed flavonoid biosynthesis genes. Among the differentially expressed selected candidates, we identified genes whose annotations were related to the circadian clock, hormonal signalling, regulation of growth, and flower development. Two genes, annotated as FLOWERING LOCUS C-like and MADS AFFECTING FLOWERING, showed strong differential expression in several comparisons. One of these two genes was upregulated in most comparisons involving dormancy release, and this gene's chromosomal position co-localized with the confidence interval of a major quantitative trait locus for the timing of bud break. These results indicate that photosynthesis and auxin transport are major regulatory nodes of apple dormancy and unveil strong candidates for the control of bud dormancy.
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Affiliation(s)
- Diogo Denardi Porto
- Centro de Pesquisa Agropecuária do Trópico Semi-Árido, Empresa Brasileira de Pesquisa Agropecuária, BR-428, Km 152, 56302-970, Petrolina, PE, Brazil
| | - Maryline Bruneau
- Institut de Recherche en Horticulture et Semences (IRHS), A, 42 rue Georges Morel, 49071 Beaucouzé Cedex, France
| | - Pâmela Perini
- Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Rua General Osório, 348, Centro, 95700-000, Bento Gonçalves, RS, Brazil
| | - Rafael Anzanello
- Fundação Estadual de Pesquisa Agropecuária, RSC-470, Km 170, 95330-000, Veranópolis, RS, Brazil
| | - Jean-Pierre Renou
- Institut de Recherche en Horticulture et Semences (IRHS), A, 42 rue Georges Morel, 49071 Beaucouzé Cedex, France
| | - Henrique Pessoa dos Santos
- Centro Nacional de Pesquisa de Uva e Vinho, Empresa Brasileira de Pesquisa Agropecuária, Rua Livramento, 515, 95700-000, Bento Gonçalves, RS, Brazil
| | - Flávio Bello Fialho
- Centro Nacional de Pesquisa de Uva e Vinho, Empresa Brasileira de Pesquisa Agropecuária, Rua Livramento, 515, 95700-000, Bento Gonçalves, RS, Brazil
| | - Luís Fernando Revers
- Centro Nacional de Pesquisa de Uva e Vinho, Empresa Brasileira de Pesquisa Agropecuária, Rua Livramento, 515, 95700-000, Bento Gonçalves, RS, Brazil
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Muranty H, Troggio M, Sadok IB, Rifaï MA, Auwerkerken A, Banchi E, Velasco R, Stevanato P, van de Weg WE, Di Guardo M, Kumar S, Laurens F, Bink MCAM. Accuracy and responses of genomic selection on key traits in apple breeding. HORTICULTURE RESEARCH 2015; 2:15060. [PMID: 26744627 PMCID: PMC4688998 DOI: 10.1038/hortres.2015.60] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits. The training population comprised 977 individuals derived from 20 pedigreed full-sib families. Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an Illumina 20K SNP array. From these data, a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application full-sib families. The application families had genotypes at 364 SNPs from a dedicated 512 SNP array, and these genotypic data were extended to the high-density level by imputation. These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values. Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19. The accuracies were strongly affected by the phenotypic distribution and heritability of traits. In the largest family, significant selection response was observed for traits with high heritability and symmetric phenotypic distribution. Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability. Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population. The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.
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Affiliation(s)
- Hélène Muranty
- Institut de Recherche en Horticulture et Semences UMR1345, INRA, SFR 4207 QUASAV, F-49071 Beaucouze, France
- ()
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Inès Ben Sadok
- Institut de Recherche en Horticulture et Semences UMR1345, INRA, SFR 4207 QUASAV, F-49071 Beaucouze, France
| | - Mehdi Al Rifaï
- Institut de Recherche en Horticulture et Semences UMR1345, INRA, SFR 4207 QUASAV, F-49071 Beaucouze, France
| | | | - Elisa Banchi
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Riccardo Velasco
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Piergiorgio Stevanato
- DAFNAE, Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, viale Università 16, 35020 Legnaro (PD), Università, degli Studi di Padova, Italy
| | - W Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Mario Di Guardo
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Satish Kumar
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 1401, Havelock North 4157, New Zealand
| | - François Laurens
- Institut de Recherche en Horticulture et Semences UMR1345, INRA, SFR 4207 QUASAV, F-49071 Beaucouze, France
| | - Marco C A M Bink
- Biometris, Wageningen University and Research Center, Wageningen, The Netherlands
- ()
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Liang L, Schwartz MD. Testing a growth efficiency hypothesis with continental-scale phenological variations of common and cloned plants. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2014; 58:1789-1797. [PMID: 23775129 DOI: 10.1007/s00484-013-0691-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 05/30/2013] [Accepted: 05/30/2013] [Indexed: 06/02/2023]
Abstract
Variation in the timing of plant phenology caused by phenotypic plasticity is a sensitive measure of how organisms respond to weather and climate variability. Although continental-scale gradients in climate and consequential patterns in plant phenology are well recognized, the contribution of underlying genotypic difference to the geography of phenology is less well understood. We hypothesize that different temperate plant genotypes require varying amount of heat energy for resuming annual growth and reproduction as a result of adaptation and other ecological and evolutionary processes along climatic gradients. In particular, at least for some species, the growing degree days (GDD) needed to trigger the same spring phenology events (e.g., budburst and flower bloom) may be less for individuals originated from colder climates than those from warmer climates. This variable intrinsic heat energy requirement in plants can be characterized by the term growth efficiency and is quantitatively reflected in the timing of phenophases-earlier timing indicates higher efficiency (i.e., less heat energy needed to trigger phenophase transitions) and vice versa compared to a standard reference (i.e., either a uniform climate or a uniform genotype). In this study, we tested our hypothesis by comparing variations of budburst and bloom timing of two widely documented plants from the USA National Phenology Network (i.e., red maple-Acer rubrum and forsythia-Forsythia spp.) with cloned indicator plants (lilac-Syringa x chinensis 'Red Rothomagensis') at multiple eastern US sites. Our results indicate that across the accumulated temperature gradient, the two non-clonal plants showed significantly more gradual changes than the cloned plants, manifested by earlier phenology in colder climates and later phenology in warmer climates relative to the baseline clone phenological response. This finding provides initial evidence supporting the growth efficiency hypothesis, and suggests more work is warranted. More studies investigating genotype-determined phenological variations will be useful for better understanding and prediction of the continental-scale patterns of biospheric responses to climate change.
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Affiliation(s)
- Liang Liang
- Department of Geography, University of Kentucky, Lexington, KY, 40506-0027, USA,
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30
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Verdu CF, Guyot S, Childebrand N, Bahut M, Celton JM, Gaillard S, Lasserre-Zuber P, Troggio M, Guilet D, Laurens F. QTL analysis and candidate gene mapping for the polyphenol content in cider apple. PLoS One 2014; 9:e107103. [PMID: 25271925 PMCID: PMC4182701 DOI: 10.1371/journal.pone.0107103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 08/12/2014] [Indexed: 11/25/2022] Open
Abstract
Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.
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Affiliation(s)
- Cindy F. Verdu
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d'Angers, EA921 Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 Quasav, PRES L'UNAM, Angers, France
| | - Sylvain Guyot
- INRA, UR1268 Biopolymères, Interactions & Assemblages, Equipe « Polyphénols, Réactivité & Procédés », Le Rheu, France
| | - Nicolas Childebrand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Muriel Bahut
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Jean-Marc Celton
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Sylvain Gaillard
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Pauline Lasserre-Zuber
- INRA-UBP, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, TN, Italy
| | - David Guilet
- Université d'Angers, EA921 Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 Quasav, PRES L'UNAM, Angers, France
| | - François Laurens
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
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Castède S, Campoy JA, García JQ, Le Dantec L, Lafargue M, Barreneche T, Wenden B, Dirlewanger E. Genetic determinism of phenological traits highly affected by climate change in Prunus avium: flowering date dissected into chilling and heat requirements. THE NEW PHYTOLOGIST 2014; 202:703-715. [PMID: 24417538 DOI: 10.1111/nph.12658] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/25/2013] [Indexed: 05/12/2023]
Abstract
The present study investigated the genetic determinism of flowering date (FD), dissected into chilling (CR) and heat (HR) requirements. Elucidation of the genetic determinism of flowering traits is crucial to anticipate the increasing of ecological misalignment of adaptative traits with novel climate conditions in most temperate-fruit species. CR and HR were evaluated over 3 yr and FD over 5 yr in an intraspecific sweet cherry (Prunus avium) F1 progeny, and FD over 6 yr in a different F1 progeny. One quantitative trait locus (QTL) with major effect and high stability between years of evaluation was detected for CR and FD in the same region of linkage group (LG) 4. For HR, no stable QTL was detected. Candidate genes underlying the major QTL on LG4 were investigated and key genes were identified for CR and FD. Phenotypic dissection of FD and year repetitions allowed us to identify CR as the high heritable component of FD and a high genotype × environment interaction for HR. QTLs for CR reported in this study are the first described in this species. Our results provide a foundation for the identification of genes involved in CR and FD in sweet cherry which could be used to develop ideotypes adapted to future climatic conditions.
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Affiliation(s)
- Sophie Castède
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - José Antonio Campoy
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - José Quero García
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - Loïck Le Dantec
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - Maria Lafargue
- INRA, UMR 1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne, F-33140, Villenave d'Ornon, France
| | - Teresa Barreneche
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - Bénédicte Wenden
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - Elisabeth Dirlewanger
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
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32
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Celton JM, Kelner JJ, Martinez S, Bechti A, Khelifi Touhami A, James MJ, Durel CE, Laurens F, Costes E. Fruit self-thinning: a trait to consider for genetic improvement of apple tree. PLoS One 2014; 9:e91016. [PMID: 24625529 PMCID: PMC3953208 DOI: 10.1371/journal.pone.0091016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 02/06/2014] [Indexed: 11/23/2022] Open
Abstract
In apple (Malus×domestica Borkh), as in many fruiting crops, fruit maintenance vs abscission is a major criteria for production profitability. Growers routinely make use of chemical thinning agents to control total fruit load. However, serious threats for the environment lead to the demand for new apple cultivars with self-thinning properties. In this project, we studied the genetic determinism of this trait using a F1 progeny derived from the cross between the hybrid INRA X3263, assumed to possess the self-thinning trait, and the cultivar 'Belrène'. Both counting and percentage variables were considered to capture the fruiting behaviour on different shoot types and over three consecutive years. Besides low to moderate but significant genetic effects, mixed models showed considerable effects of the year and the shoot type, as well as an interaction effect. Year effect resulted mainly from biennial fruiting. Eight Quantitative Trait Locus (QTL) were detected on several linkage groups (LG), either independent or specific of the year of observation or the shoot type. The QTL with highest LOD value was located on the top third of LG10. The screening of three QTL zones for candidate genes revealed a list of transcription factors and genes involved in fruit nutrition, xylem differentiation, plant responses to starvation and organ abscission that open new avenues for further molecular investigations. The detailed phenotyping performed revealed the dependency between the self-thinning trait and the fruiting status of the trees. Despite a moderate genetic control of the self-thinning trait, QTL and candidate genes were identified which will need further analyses involving other progenies and molecular investigations.
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Affiliation(s)
- Jean-Marc Celton
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro Team «Architecture et Fonctionnement des Espèces Fruitières», Montpellier, France
- Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), AgroCampus-Ouest, Université d’Angers, SFR 4207 QUASAV, Beaucouzé, France
| | - Jean-Jacques Kelner
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro Team «Architecture et Fonctionnement des Espèces Fruitières», Montpellier, France
| | - Sébastien Martinez
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro Team «Architecture et Fonctionnement des Espèces Fruitières», Montpellier, France
| | - Abdel Bechti
- Pépinières et Roseraies G. Delbard, Commentry, France
| | - Amina Khelifi Touhami
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro Team «Architecture et Fonctionnement des Espèces Fruitières», Montpellier, France
| | | | - Charles-Eric Durel
- Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), AgroCampus-Ouest, Université d’Angers, SFR 4207 QUASAV, Beaucouzé, France
| | - François Laurens
- Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), AgroCampus-Ouest, Université d’Angers, SFR 4207 QUASAV, Beaucouzé, France
| | - Evelyne Costes
- Institut National de la Recherche Agronomique (INRA), UMR 1334, AGAP CIRAD-INRA-Montpellier SupAgro Team «Architecture et Fonctionnement des Espèces Fruitières», Montpellier, France
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33
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Romeu JF, Monforte AJ, Sánchez G, Granell A, García-Brunton J, Badenes ML, Ríos G. Quantitative trait loci affecting reproductive phenology in peach. BMC PLANT BIOLOGY 2014; 14:52. [PMID: 24559033 PMCID: PMC3941940 DOI: 10.1186/1471-2229-14-52] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/18/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The reproductive phenology of perennial plants in temperate climates is largely conditioned by the duration of bud dormancy, and fruit developmental processes. Bud dormancy release and bud break depends on the perception of cumulative chilling and heat during the bud development. The objective of this work was to identify new quantitative trait loci (QTLs) associated to temperature requirements for bud dormancy release and flowering and to fruit harvest date, in a segregating population of peach. RESULTS We have identified QTLs for nine traits related to bud dormancy, flowering and fruit harvest in an intraspecific hybrid population of peach in two locations differing in chilling time accumulation. QTLs were located in a genetic linkage map of peach based on single nucleotide polymorphism (SNP) markers for eight linkage groups (LGs) of the peach genome sequence. QTLs for chilling requirements for dormancy release and blooming clustered in seven different genomic regions that partially coincided with loci identified in previous works. The most significant QTL for chilling requirements mapped to LG1, close to the evergrowing locus. QTLs for heat requirement related traits were distributed in nine genomic regions, four of them co-localizing with QTLs for chilling requirement trait. Two major loci in LG4 and LG6 determined fruit harvest time. CONCLUSIONS We identified QTLs associated to nine traits related to the reproductive phenology in peach. A search of candidate genes for these QTLs rendered different genes related to flowering regulation, chromatin modification and hormone signalling. A better understanding of the genetic factors affecting crop phenology might help scientists and breeders to predict changes in genotype performance in a context of global climate change.
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Affiliation(s)
- José F Romeu
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), La Alberca, Murcia, Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Valencia, Spain
| | - Gerardo Sánchez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Valencia, Spain
| | - Jesús García-Brunton
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), La Alberca, Murcia, Spain
| | - María L Badenes
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
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Dambreville A, Lauri PÉ, Trottier C, Guédon Y, Normand F. Deciphering structural and temporal interplays during the architectural development of mango trees. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2467-80. [PMID: 23585668 DOI: 10.1093/jxb/ert105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Plant architecture is commonly defined by the adjacency of organs within the structure and their properties. Few studies consider the effect of endogenous temporal factors, namely phenological factors, on the establishment of plant architecture. This study hypothesized that, in addition to the effect of environmental factors, the observed plant architecture results from both endogenous structural and temporal components, and their interplays. Mango tree, which is characterized by strong phenological asynchronisms within and between trees and by repeated vegetative and reproductive flushes during a growing cycle, was chosen as a plant model. During two consecutive growing cycles, this study described vegetative and reproductive development of 20 trees submitted to the same environmental conditions. Four mango cultivars were considered to assess possible cultivar-specific patterns. Integrative vegetative and reproductive development models incorporating generalized linear models as components were built. These models described the occurrence, intensity, and timing of vegetative and reproductive development at the growth unit scale. This study showed significant interplays between structural and temporal components of plant architectural development at two temporal scales. Within a growing cycle, earliness of bud burst was highly and positively related to earliness of vegetative development and flowering. Between growing cycles, flowering growth units delayed vegetative development compared to growth units that did not flower. These interplays explained how vegetative and reproductive phenological asynchronisms within and between trees were generated and maintained. It is suggested that causation networks involving structural and temporal components may give rise to contrasted tree architectures.
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Legave JM, Blanke M, Christen D, Giovannini D, Mathieu V, Oger R. A comprehensive overview of the spatial and temporal variability of apple bud dormancy release and blooming phenology in Western Europe. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2013; 57:317-31. [PMID: 22610120 DOI: 10.1007/s00484-012-0551-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 04/17/2012] [Accepted: 04/17/2012] [Indexed: 05/26/2023]
Abstract
In the current context of global warming, an analysis is required of spatially-extensive and long-term blooming data in fruit trees to make up for insufficient information on regional-scale blooming changes and determinisms that are key to the phenological adaptation of these species. We therefore analysed blooming dates over long periods at climate-contrasted sites in Western Europe, focusing mainly on the Golden Delicious apple that is grown worldwide. On average, blooming advances were more pronounced in northern continental (10 days) than in western oceanic (6-7 days) regions, while the shortest advance was found on the Mediterranean coastline. Temporal trends toward blooming phase shortenings were also observed in continental regions. These regional differences in temporal variability across Western Europe resulted in a decrease in spatial variability, i.e. shorter time intervals between blooming dates in contrasted regions (8-10-day decrease for full bloom between Mediterranean and continental regions). Fitted sequential models were used to reproduce phenological changes. Marked trends toward shorter simulated durations of forcing period (bud growth from dormancy release to blooming) and high positive correlations between these durations and observed blooming dates support the notion that blooming advances and shortenings are mainly due to faster satisfaction of the heating requirement. However, trends toward later dormancy releases were also noted in oceanic and Mediterranean regions. This could tend toward blooming delays and explain the shorter advances in these regions despite similar or greater warming. The regional differences in simulated chilling and forcing periods were consistent with the regional differences in temperature increases.
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Cooke JEK, Eriksson ME, Junttila O. The dynamic nature of bud dormancy in trees: environmental control and molecular mechanisms. PLANT, CELL & ENVIRONMENT 2012; 35:1707-28. [PMID: 22670814 DOI: 10.1111/j.1365-3040.2012.02552.x] [Citation(s) in RCA: 298] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In tree species native to temperate and boreal regions, the activity-dormancy cycle is an important adaptive trait both for survival and growth. We discuss recent research on mechanisms controlling the overlapping developmental processes that define the activity-dormancy cycle, including cessation of apical growth, bud development, induction, maintenance and release of dormancy, and bud burst. The cycle involves an extensive reconfiguration of metabolism. Environmental control of the activity-dormancy cycle is based on perception of photoperiodic and temperature signals, reflecting adaptation to prevailing climatic conditions. Several molecular actors for control of growth cessation have been identified, with the CO/FT regulatory network and circadian clock having important coordinating roles in control of growth and dormancy. Other candidate regulators of bud set, dormancy and bud burst have been identified, such as dormancy-associated MADS-box factors, but their exact roles remain to be discovered. Epigenetic mechanisms also appear to factor in control of the activity-dormancy cycle. Despite evidence for gibberellins as negative regulators in growth cessation, and ABA and ethylene in bud formation, understanding of the roles that plant growth regulators play in controlling the activity-dormancy cycle is still very fragmentary. Finally, some of the challenges for further research in bud dormancy are discussed.
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Affiliation(s)
- Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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Fabbrini F, Gaudet M, Bastien C, Zaina G, Harfouche A, Beritognolo I, Marron N, Morgante M, Scarascia-Mugnozza G, Sabatti M. Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar. BMC PLANT BIOLOGY 2012; 12:47. [PMID: 22471289 PMCID: PMC3378457 DOI: 10.1186/1471-2229-12-47] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 04/03/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of P. nigra with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions. RESULTS Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E) interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes.Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL) for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5), the transition from shoot to bud (date1.5), the duration of bud formation (subproc1) and bud maturation (subproc2)) eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and P. trichocarpa genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs). These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set. CONCLUSIONS This study provides a better understanding of the physiological and genetic dissection of bud set in poplar. The putative QTL identified will be tested for associations in P. nigra natural populations. The identified QTL and CGs will also serve as useful targets for poplar breeding.
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Affiliation(s)
- Francesco Fabbrini
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
| | - Muriel Gaudet
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
| | - Catherine Bastien
- INRA, UR 0588, National Institute for Agricultural Research, Orléans 2 F-45075, France
| | - Giusi Zaina
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze, Udine 33100, Italy
| | - Antoine Harfouche
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
| | - Isacco Beritognolo
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
- Institute for Mediterranean Agriculture and Forest Systems, National Research Council, Via Madonna Alta, Perugia 06128, Italy
| | - Nicolas Marron
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
- INRA, UMR 1137, INRA-Nancy University, Champenoux F-54280, France
| | - Michele Morgante
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze, Udine 33100, Italy
- Istituto di Genomica Applicata, Via J. Linussio 51, Udine 33100, Italy
| | - Giuseppe Scarascia-Mugnozza
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
- Department of Agronomy, Forestry and Land use, Agricultural Research Council, Via del Caravita, Roma 00186, Italy
| | - Maurizio Sabatti
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
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