BREEDING AND GENETICS OF LANDSCAPE ROSES ADAPTED TO A HUMID SUBTROPICAL CLIMATE

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: ACTIVE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1023882
• Project Start Date: Jul 27, 2020
• Project End Date: Jul 27, 2025
• Program Code: [(N/A)]- (N/A)

Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001

Performing Department
Horticultural Science

Non Technical Summary
The goal of the rose breeding program at Texas A&M University is to develop sustainable garden varieties that combine high ornamental value with adaptation humid subtropical climates. The major challenges are to bring together resistance against fungal diseases (black spot and Cercospora leaf spot), resistance to the rose rosette virus (RRV), heat tolerance, and high ornamental quality. For this, our strategy is to exploit TAMU diploid germplasm exhibiting adaptation to the environmental conditions present in Texas through conventional breeding schemes that are coupled with the use genomics-based approaches to further enhance disease resistance, abiotic stress tolerance, and ornamental quality of tetraploid germplasm. Furthermore, an effort will continue to better understand the genetic basis of traits of ornamental importance and to apply this information on a plant breeding context.

Animal Health Component

60%

Research Effort Categories

Basic

40%

Applied

60%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
202	2110	1080	20%
202	2110	1081	30%
203	2110	1080	20%
203	2110	1081	30%

Knowledge Area
203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 202 - Plant Genetic Resources;

Subject Of Investigation
2110 - Ornamental trees and shrubs;

Field Of Science
1081 - Breeding; 1080 - Genetics;

Keywords

rosa

genetics

genomics

breeding

diversity

disease resistance

adaptation

Goals / Objectives
The goal of the rose breeding program at Texas A&M University is to develop sustainable garden varieties that combine high ornamental value with adaptation humid subtropical climates. The major challenges are to bring together resistance against fungal diseases (black spot and Cercospora leaf spot), resistance to the rose rosette virus (RRV), heat tolerance, and high ornamental quality.Objectives:Develop landscape rose germplasm adapted to humid subtropical conditionsBuild on TAMU diploid rose germplasm with resistance to blackspotStack blackspot resistance QTL/genes that have been identifiedIncorporate Cercospora leaf spot resistance toblackspot resistant backgroundsCouple rose rosette disease resistance with blackspot and Cercospora resistance and exploit QTL that have been identifiedEnhance adapted germplasm with respect to superior ornamental and architectural traitsFocus on development of compact bush typesSelect for high flower productivity during warm conditionsIncorporate a wider range of flower colors and types as well as fragranceEvaluate genomic prediction approaches to improve parent selection and increase selection accuracyConduct genetics research in roses.Understand the genetic structure of rose germplasm to mine untapped genetic diversity for breedingIdentify and characterize genetic determinants of rose rosette disease, blackspot, and Cercospora leaf spot resistance, and other economically important diseasesIdentify and characterize genetic determinants of flower productivity, flower color, and plant architectureExplore gene editing techniques to enhance traits in rose germplasm

Project Methods
The Texas A&M rose breeding and genetics team working with collaborators, from the US and abroad, has made significant inroads on unveiling the genetic basis of some traits of interest and setting the state to use of marker/genomics-based tools in variety development. A protocol to use genotype-by-sequencing (GBS) technology for the construction of a comprehensive diploid rose linkage maps is in place (Yan et al., 2018). A pipeline to use the WagRhSNP 68K Axiom array platform (Bourke et al., 2019; Vukasvljev et al., 2016; Zych et al., 2019) for high density map construction in tetraploids is also in place. In turn, these capabilities have been used to identify quantitative trait locus/loci (QTL) using various mapping populations. Inter-related diploid rose populations have been used to identify QTL for black spot and Cercospora leaf spot resistance (Bink et al. 2014; Kang, 2020; Yan et al., 2019; Young, 2020). Similarly, QTL for resistance to blackspot and Cerscopora have been identified using tetraploid populations (Hackett et al., 2013; 2014; Lau et al., 2020a). Studies in both diploid and tetraploid populations have also revealed QTL for flower productivity and plant architectural traits (Lau et al. 2020a; Young 2020). These efforts complement work performed elsewhere (Debener, 2019; Smulders et al. 2019) and represent starting points to use marker aided selection for the construction of new genetic architectures where factors for resistance to disease and ornamental quality traits can be combined/stacked.As stated earlier, our strategy will be to combine the generally superior disease resistance in diploid TAMU germplasm (Byrne et al., 2007; Byrne et al., 2010; Dong et al., 2017) with tetraploid germplasm with superior horticultural and flower characteristics. This will be achieved by crossing diploids with tetraploids and/or doubling the chromosomes of the diploid selections (Byrne and Ma, 2003; Ma et al., 1997) before crossing to tetraploid germplasm (Byrne, 2007; Byrne, 2015). At the tetraploid level, we will exploit germplasm with black spot resistance (Debener, 2019; Zurn et al., 2018; 2020) and combine it with material with superior bush and flower characteristics.The basic breeding cycle is four years followed by three years of commercial testing coupled with mass propagation before release. Thus, a new cultivar can be produced in seven to eight years (Byrne et al., 2018). In year 1 of this cycle, seed is produced from artificial hybridizations in the greenhouse. In year 2, hybrid seeds are planted, seedlings are grown, and selected in the greenhouse for traits of high heritability such as basic flower/plant characteristics and resistance to powdery mildew. In years 3 and 4, selections are tested under field conditions to assess overall adaptation and resistance to key diseases (black spot and Cercospora). The best selections can then be entered into a three-year multisite commercial trial before the final decision is made on their release. For the introgression of a new trait such as rose rosette disease resistance, additional time will be required depending on the source of resistance that is used (Byrne et al., 2018). The rose breeding pipeline at Texas A&M has selections at all stages of development. Thus, all of the activities outlined above take place every year where the pertinent technological intervention can be applied.In order to incorporate genomics tools in some aspects of the variety development process, we will explore the use of DNA-based markers to stack a major partial black spot resistance factor on chromosome 3 (Yan et al., 2019; Young, 2020; Lau et al., 2020) with the black spot resistance genes Rdr1 (Menz et al., 2018; Rouet et al., 2020), Rdr3 (Zurn et al., 2020), and Rdr4 (Zurn et al., 2018). Individuals that have combinations of Rdr4 and the partial black spot resistance factor on chromosome 3 in tetraploid germplasm have been identified and will be used in combination of sources carrying Rdr1 to initiate this effort. Once Cercospora leaf spot resistance QTL have been better characterized, these will be added to the pyramiding effort. Similarly, putative QTL for tolerance to symptom development in tetraploid germplasm infected with the rose rosette virus (Lau et al. 2020b) will be incorporated in pyramiding efforts after these have been validated. In all cases, we will apply strong selection for superior horticultural and flower characteristics of the derived progenies. In addition to approaches that leverage QTL, we will assess the use of predictive tools (Endelman et al. 2018; Ersoz et al. 2020) to increase seedling selection rates in the greenhouse or at early field evaluation stages, and better identify unique recombinants and parental lines. This should lead to increased genetic gain, improved breeding efficiency, and reduced costs if applied to reducing breeding cycle times.Other opportunities exist to manipulate and modify genes in roses as well as to apply genomics-based approaches to better understand underlying biological mechanisms and guide selection of traditionally bred roses. Thus, efforts will continue on using populations and germplasm panels to better understand the genetic structure of rose breeding germplasm and to identify/characterize genetic determinants of disease resistance (black spot, Cercospora, and rose rosette disease), flower productivity, and ornamental value (Smulders et al. 2019). Similarly, partnerships will be explored to leverage genome-editing technologies to manipulate traits (Ahn et al., 2020).

Progress 07/27/20 to 09/30/20

Outputs
Target Audience:Target audience: Rose growers, the rose industry, and gardeners in Texas and other areas with similar environments. Effort: Variety releases and information developed by rose breeding program will be distributed via talks at various industry meetings, online outlets, Agrilife Extension, TAMU Agricultural Communications as well as through commercial partners. Target audience: The rose breeding and genetics research community. Effort: The scientific information on rose genetics will be distributed via referred scientific journals, national/international scientific meetings, and articles in the popular press. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Graduate students and postdocs in the program have been allowed to participate and present research at various professional meetings including the Texas A&M Plant Breeding Symposium (College Station, TX), Plant Animal Genome XXVIII (San Diego, CA), and the 10th Rose Genomics Conference (Barcelona, Spain, Virtual). How have the results been disseminated to communities of interest?Research results have been presented at local, regional, national and international level professional meetings including the Texas A&M Plant Breeding Symposium (College Station, TX), the 32nd Annual Texas Plant Protection Conference (Conroe, TX, Virtual), Plant Animal Genome XXVIII (San Diego, CA), and the 10th Rose Genomics Conference (Barcelona, Spain, Virtual). What do you plan to do during the next reporting period to accomplish the goals?We will develop populations that combine the major partial black spot resistance factor on linkage group (LG) 3 and the black spot resistance genes Rdr1 (LG1) and Rdr4 (LG5). We will also identify material with Rdr3 and develop a strategy to add this gene to our pyramiding efforts.Besides gene stacking efforts, we will continue work to better understand the genetic structure of rose breeding germplasm and to identify/characterize other genetic determinants of disease resistance (black spot, Cercospora, and rose rosette disease), flower productivity, and ornamental value. Once key QTL have been better characterized and validated, these will be added to our gene pyramiding/breeding effort.

Impacts
What was accomplished under these goals? The focus of the rose breeding program at Texas A&M University is to develop sustainable garden varieties with good adaptation and high ornamental value. Our strategy is to combine the generally superior disease resistance in diploid TAMU germplasm with tetraploid germplasm with superior horticultural and flower characteristics. This goal is being pursued by using DNA-based markers to stack a major partial black spot resistance factor on linkage group (LG) 3 with the black spot resistance genes Rdr1 (LG1), Rdr3 (LG6), and Rdr4 (LG5). Individuals from the 'Brite Eyes x My Girl' population with combinations of Rdr4 and the partial black spot resistance factor on LG3 have been identified. Similarly, individuals that carry Rdr1 from other populations have been identified. These materials will be intercrossed to initiate this blackspot resistance stacking effort. Similar work to incorporate Rdr3 is underway. Concerning genetics research to better understand the genetic basis of traits of ornamental value, we have various diploid and tetraploid rose mapping populations currently under study. These will be used to identify genetic determinants of resistance to cercospora leaf spot and the rose rosette virus as well as factors that control plant architecture, flower productivity, and flower color. As these factors are identified and validated, they will be incorporated into our breeding efforts. We are also exploring partnerships to leverage genome-editing technologies to manipulate traits in roses.

Publications

• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Riera-Lizarazu, O., P. Klein, M. Yan, Z. Rawandoozi, E. Young, S. Kang, J. Lau, and D. Byrne. 2020. Towards Genomics-Assisted Breeding in Roses: Improving Resistance to Fungal Diseases and Flower Productivity. 10th Rosaceae Genomics Conference, December 9-11 and 16-18, Barcelona, Spain (Virtual). C0137
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Riera-Lizarazu, O., P. Klein, and D. Byrne. 2020. Towards Genomics-Assisted Rose Breeding in Texas. 32nd Annual Texas Plant Protection Conference. December 8-10, Conroe, TX (Virtual)
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Chhabra, B., O. Riera-Lizarazu, S. Kianian, J.M. Leonard, E. Paux, and V.K. Tiwari. 2020. A deletion based high-throughput functional genomics resource for wheat. In: Abstracts of Plant & Animal Genome XXVIII, January 11-15, San Diego, CA. PE1084
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Lau, J., E. Young, N. Patterson, P.E. Klein, O. Riera-Lizarazu, and D.H. Byrne. 2020. Genetic characterization of two tetraploid rose bi-parental mapping populations In: Abstracts of Plant & Animal Genome XXVIII, January 11-15, San Diego, CA. PE0517
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Young, E., J. Lau, P.E. Klein, O. Riera-Lizarazu, and D.H. Byrne. 2020. Association mapping of disease resistance and architecture traits in diploid rose cultivars. In: Abstracts of Plant & Animal Genome XXVIII, January 11-15, San Diego, CA. PE0518
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Lau, J., E. Young, N. Patterson, P.E. Klein, O. Riera-Lizarazu, and D.H. Byrne. 2020. Genetic characterization of two autotetraploid rose mapping populations. Texas A&M Plant Breeding Symposium, February 20, College Station TX.
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Young, E., J. Lau, P.E. Klein, O. Riera-Lizarazu, and D.H. Byrne. 2020. Association mapping of disease resistance and architecture traits in diploid rose cultivars and families. Texas A&M Plant Breeding Symposium, February 20, College Station TX.