AdRoot: Genetic control of adventitious rooting in horticultural crops

The aim of the proposed "AdRoot" project is to understand the genetic control of adventitious rooting and to identify molecular markers and beneficial alleles that will allow adventitious rooting to be controlled to the benefit of breeding in horticultural crops. Adventitious roots arise from plant stems during normal plant development or in response to environmental stresses such as flooding and wounding. In annual vegetable crops, including the grafted crops of the Solanaceae (tomato, pepper) and Cucurbitaceae (melon, watermelon) families, root system function relies partially on adventitious roots that develop from the hypocotyl (basal roots) or from the main stem, and this makes a contribution to root vigour which is largely undefined. In addition, propagation in perennial crops, especially from the Rosaceae family (including apple, plum, cherry, raspberries, strawberries) is dependent on the formation of adventitious roots from cuttings, runners (as in strawberries) and from nodal explants used for micropropagation. We will identify the genetic factors that control adventitious rooting in a crop from Solanaceae (tomato) and from Rosaceae (raspberry) through a programme of molecular genetic analysis, and we will conduct a comparative evaluation of genetic regulation of adventitious root formation in these key plant families. The understanding derived from this study will be suitable for improving the processes of (i) breeding of vegetable rootstocks to control root (and so scion) vigour, and (ii) ensuring that new cultivars within the Rosaceae family can be efficiently propagated. The project will involve a global seed company interested in selling more vegetable rootstock seeds, and a company involved in producing and breeding new soft fruit cultivars. The project will also generate new genomic and genetic resources to accelerate raspberry breeding.

The aim of the proposed "AdRoot" project is to understand the genetic control of adventitious rooting (AR) and to identify molecular markers and beneficial alleles that will allow AR to be controlled to the benefit of breeding in horticultural crops. AR formation from the hypocotyl is important for rootstock vigour in grafted annual crops like tomato, and AR formation is essential for propagation in all perennial crops. In tomato we recently mapped the classical "aerial root" mutation to a single gene, and discovered that a second locus is required for full expression of the mutant phenotype. We will identify this second locus and study the interaction between the two genes. We have obtained additional sources of genetic variation in tomato for adventitious root formation from a global seed company and from international collaborators and we will map the genes responsible using a powerful combination of next generation sequencing, bulked segregant analysis and conventional genetic mapping. The knowledge gained will be used as a platform to understand the genes and regulatory networks that define variation in AR development in raspberry as a model perennial crop and as a crop that has evolved a unique strategy of vegetative reproduction through AR formation on the apices of downward curving primocanes. By direct collaboration with a UK-based soft fruit breeding company, we will perform high resolution QTL analysis for AR traits, using an F1 mapping population in this outbreeding species, backed-up by an Oxford Nanopore raspberry genome assembly, and a high density genetic map generated from genotype-by-sequencing. Candidate genes will be prioritised through comparative genomic analysis and validated for use in marker assisted selection in alternative raspberry F1 populations available at the breeding company.

The project involves Cranfield University (CU) working with Syngenta seeds (SG), a global seed company active in breeding of annual vegetable crops including tomato, and with Edward Vinson Ltd (EV) a breeder and producer of soft fruit associated with the BerryWorld group. The two project industry partners will provide essential in-kind contributions to the research program, and the proposed project is therefore conceived to deliver understanding and genetic markers of value to crop improvement programmes that constantly strive to create better crop cultivars. Improved varieties have immense value to breeders (sales), growers (improved yield, quality and profits), the environment (reduced inputs and increased resource use efficiency and sustainability) and to consumers (higher quality, lower prices, improved health). The project aims to discover genes that control adventitious rooting, a process that is vital for propagation of perennial crops, but that is potentially also linked to general capacity for general root vigour through production of roots directly from the epicotyl and the hypocotyl stem.
Tomato fruit are grown predominantly as grafts between rootstock and scion, and breeding for rootstock vigour is a major target for many vegetable seed companies including SG. Use of rootstocks has grown rapidly in Europe as a means to control soil-borne diseases since the withdrawal of methyl bromide as a soil fumigant. This has opened opportunities to deliver other traits via rootstocks and to extend their use to sectors where there are barriers to uptake, e.g. processing tomato where the cost of grafted transplants is not yet justified by the benefits, and pepper where there is weak market penetration. SG also seeks to increase market share of tomato rootstock seed sales globally. Berry consumption in the UK is undergoing a period of significant growth due to improved quality and reliability of supply and changing customer demands. It is therefore timely to invest in research in Rubus crops to ensure UK breeders and growers remain competitive. Adventitious rooting is a key trait in all perennial crops as it is an essential process in propagation, and is especially important in raspberry where there is a high cultivar rotation and new bare rooted primocanes are planted annually. In this project we will work closely with the two industry project partners, and this will provide a clear mechanism to transfer knowledge to commercial breeding activities. In addition, we will present work at crop conferences specific to Solanaceae and Rosaceae which are attended by a mixture of academics and breeders, and will communicate using the trade press and press releases with growers and consumers, respectively.
Research students at Cranfield University will benefit since we will use the project to kick-start a series of annual workshops between students and the breeding industry to improve student understanding of commercial practice and to introduce students to potential employers.