For over 70 years, the "Green Revolution" spurred by dwarfing traits has provided a new pathway to ensure global food security, particularly in cereal crops. In fact, as early as the beginning of the 20th century, the introduction of dwarfing traits in woody and vine crops to achieve high-density planting had already caught the attention of breeders. However, unlike herbaceous crops such as cereals, achieving dwarfing in woody and vine crops relies heavily on rootstocks.
The latest breakthrough in apple tree dwarfing through standardization of wide-row and close-planting spacing was recently published online by a team led by Professor Zhenhai Han from the College of Horticulture at China Agricultural University. This study, featured in the journal Nature Genetics, marks the first time a comprehensive investigation into global fruit tree rootstocks has been published, laying the groundwork for molecular-designed breeding of dwarfing rootstocks in apple and other woody economic crops, accelerating the realization of a "green revolution."
Rootstocks: The Key to Dwarfing Apples
China is the world's largest producer of apples, accounting for over 56% of global production and over 40% of planting area. According to Dr. Fengwang Ma, Chief Scientist of the National Apple Industry Technology System and professor at Northwest A&F University, one of the major challenges facing the healthy and sustainable development of the apple industry is the decreasing and aging agricultural workforce, highlighting the need for mechanization and simplified management practices.
Since the 1910s, when the East Malling Research Station in the UK bred the M-series apple dwarfing rootstocks, the widespread adoption of dwarfing and close planting has significantly increased the productivity of apples worldwide, offering effective solutions for the healthy and sustainable development of the apple industry.
Dr. Wei Li, associate professor at China Agricultural University and the first author of the paper, explains that most fruit trees and other economic crops are graft unions composed of scion varieties (above-ground shoots) and rootstocks (below-ground root systems). The characteristics and interactions of the scion and rootstock determine the growth, development, and yield quality of fruit trees. Dwarfing of fruit trees and other economic crops primarily relies on rootstocks with dwarfing effects, which, when grafted with scion varieties, result in fewer long branches, more short branches, and weakened overall tree vigor.
"Therefore, the key to tree dwarfing lies in the rootstock. With dwarfing rootstocks, trees can be dwarfed, becoming smaller and shorter," says Professor Zhenhai Han, the corresponding author of the paper. Rootstocks serve essential functions such as providing structural support, nutrient and water absorption, and secretion of organic substances into the rhizosphere, thereby enhancing the resilience and adaptability of perennial fruit trees and other economic crops.
Establishment of Standardized Demonstration Gardens for Dwarfing and High-Density Planting of Apple Orchards. Photo by Wang Xiaoqing.
The introduction of dwarfing traits can effectively control the growth vigor of fruit trees and other cash crops, maximizing land use efficiency and increasing yield per unit area to the fullest extent. Widening the spacing between rows optimally utilizes solar energy and significantly enhances fruit quality. With reduced tree height, some are merely half or two-thirds the height of conventionally grown trees. The combination of widened row spacing and consistent interplanting facilitates mechanized operations, reduces manual labor, and decreases the labor intensity for fruit growers, making orchard management more convenient and efficient.
"Therefore, the cultivation system of dwarfing and high-density planting, due to its ability to achieve both economic and ecological benefits, is a global trend in the production of fruit trees and other cash crops. In the transformation and upgrading of production methods for fruit trees and other cash crops, it is equivalent to a green revolution for crops," said Zhang Shaoling, Academician of the Chinese Academy of Engineering and Professor at Nanjing Agricultural University.
Although efforts have been made to breed rootstocks with dwarfing traits for major fruit trees and other cash crops, it is primarily apple orchards and a small portion of pear orchards that have seen large-scale application in production.
Since the 1970s, China has imported dwarfing rootstocks such as M9, M26, B series, and CG series from abroad and initiated the breeding of dwarfing rootstocks for apples in China. New dwarfing rootstock varieties such as the 'Zhongzhen' series, SH series, and Qingzhen series have been successfully bred. "These dwarfing rootstocks have been widely used in the past 20 years, increasing the proportion of dwarfing and high-density planting of Chinese apples from 2% in the early 21st century to nearly 20% now," said Wang Yi, Professor at China Agricultural University and co-corresponding author of the paper.
"Compared with developed countries where over 80% of fruit trees are cultivated using dwarfing and high-density planting techniques, there is still a significant gap. Efficient breeding of dwarfing, disease-resistant rootstocks with strong adaptability to local conditions is of great significance for ensuring the healthy and sustainable development of China's apple industry," said Han Zhenhai.
Resource Collection: Deciphering the Secrets of Rootstocks
However, the traditional breeding cycle for apple rootstocks is 20 to 30 years. The decoding of dwarfing mechanisms in rootstocks and the discovery of key regulatory genes are still in the exploratory stage. The published apple genome so far only includes cultivated varieties and a small number of wild relatives, such as Gala, Xinjiang wild apples, and forest apples, lacking the genome of apple dwarfing rootstocks. Therefore, "deciphering the genome of apple dwarfing rootstocks is of great value for achieving molecular design breeding of apple rootstocks and promoting the modern transformation of apple planting and cultivation models," said Han Zhenhai.
"Apple has seen significant growth in harvest index, largely attributed to the widespread adoption of clonal dwarfing rootstocks," explained Professor Zhang Dong from Northwest A&F University. In the early 20th century, the M and MM series clonal rootstocks developed by the East Malling Research Station in the UK had a lasting impact on the industry. Over the past century, numerous clonal rootstock varieties with diverse genetic backgrounds have been bred by apple rootstock breeding institutions worldwide, such as the R series and CG series in the United States, the B series in the former Soviet Union, and the 'Zhongzhen' series, SH series, and Qingzhen series in China.
Zhang Hengtao, co-first author of the paper and researcher at the Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, told China Science News that the use of clonal rootstocks is particularly important. Through methods such as tissue culture, grafting, and cutting propagation, clonal rootstocks are reproduced without sexual hybridization, ensuring consistent genetic characteristics among offspring, which guarantees uniformity in tree growth, form, yield, and fruit quality, as well as neat orchard appearance, easy management, and suitability for large-scale production in modern orchards.
Among these, M9 is the most widely used dwarfing rootstock in the world, with nearly 90% of apple orchards in Western Europe grafted onto M9. Therefore, it serves as the standard rootstock for studying the induction mechanism of dwarfing phenotypes. "Meanwhile, MM106 is a semi-dwarfing rootstock bred by crossing M series rootstocks. Comparative analysis of the genomes of M9 and MM106 may reveal candidate genetic variations associated with dwarfing characteristics," said Han Zhenhai.
Li Hui, co-first author of the paper and doctoral student at China Agricultural University, told China Science News that to clarify the systematic evolutionary relationships between rootstock varieties and the genetic background of rootstocks with wild and cultivated species, they collected clonal rootstock materials from apples worldwide.
Since different rootstock varieties possess different dwarfing, disease resistance, cold resistance, drought resistance, and other characteristics, understanding the systematic evolutionary relationships and genetic relationships between apple rootstock varieties can fully exploit and utilize apple genetic resources, help breeders better understand the genetic background differences and genetic variation patterns among different rootstock varieties, select breeding parents targetedly, improve rootstock breeding efficiency, and provide scientific basis for selecting suitable rootstock varieties and graft combinations in production.
Based on this, they constructed a phylogenetic tree and found that apple rootstocks simultaneously accept genetic introgression from wild and cultivated species.
Promoting the Green Revolution in Forestry and Fruit Industry
"Dwarfing rootstocks have already changed the way apples are cultivated, yet the genetic basis for inducing dwarfing in dwarfing rootstocks is still not well understood," said Han Zhenhai. Therefore, the team assembled chromosome-level, nearly complete, and haplotype-resolved genomes for the dwarfing rootstock M9, the semi-dwarfing rootstock MM106, and Fuji, a common apple cultivar. They successfully discovered an insertion sequence present only in the M9 genome and further revealed its potential as a key genetic code for inducing dwarfing in apple rootstocks.
Grafting is a widely used practice in horticulture, and while grafting onto dwarfing rootstocks induces corresponding dwarfing changes in the scion, its genetic mechanism remains largely unknown. Previous studies have suggested that large molecules, such as mRNA, transported through vascular tissue between rootstock and scion play a crucial role in graft-induced phenotypic changes. However, the identification of mRNA transfer between rootstock and scion remains a technical challenge.
Results of Grafting Dwarfing Trees. (Image by Hong Zhang)
To address this issue, the team developed a bioinformatics pipeline called "RNAGlass" on the basis of assembling the high-quality genome of the Fuji apple variety and identified mRNA transcripts transferred between the scion and the rootstock during the critical period of dwarfing, thereby significantly promoting the comprehensive elucidation of the molecular mechanism of dwarfing in rootstocks.
According to Li Wei, deciphering the genes and molecular mechanisms of dwarfing in rootstocks provides a genetic foundation for the molecular design and breeding of dwarfing rootstocks in woody economic crops such as apples, accelerating the realization of a "green revolution" and laying a solid theoretical foundation. In the future, breeders will be able to quickly screen dwarf individuals from a large pool of materials, effectively avoiding the tedious and lengthy process of progeny selection in traditional breeding, greatly saving time and resources, significantly shortening the breeding cycle, and improving breeding efficiency.
"It is expected that the traditional 20-30 year breeding cycle for apple rootstocks can be shortened to 10-15 years, realizing the rapid and efficient breeding of new dwarfing rootstock varieties for apples and providing widely available dwarfing, multi-resistant asexual line apple rootstock varieties for China's major apple producing areas," said Han Zhenhai. He also stated that dense planting of dwarfing trees will promote the development of the fruit industry towards mechanization and intelligence, improving orchard production efficiency and management level.
However, Han Zhenhai emphasized that since molecular breeding for apples is still in its infancy internationally, there are still many difficulties to be addressed in the future, including fully exploring apple resistance genes, and the transgenic/gene editing technology system for different strains of ripening apples (rootstocks).
Meanwhile, there is a demand for dwarfing in major fruit trees and other economic crops, especially woody fruit trees and some tree species with tall or vigorous growth, such as pears, peaches, plums, cherries, citrus fruits, chestnuts, walnuts, etc. The dwarfing genes discovered in this research exhibit certain conservatism in controlling plant vigor in fruit trees. Therefore, "this is expected to initiate the efficient breeding of dwarfing rootstocks in woody economic crops and promote a true green revolution in the fruit industry," said Han Zhenhai.
Related Paper Information: https://doi.org/10.1038/s41588-024-01657-2
