For over 70 years, the dwarfing trait has sparked a "green revolution" in cereal crops, offering a new avenue to ensure global food security. In fact, as early as the beginning of the 20th century, breeders had their sights set on introducing dwarfing traits into woody and vining economic crops for high-density planting. However, unlike herbaceous crops such as cereals, achieving dwarfing in woody and vining crops relies heavily on rootstocks.
The latest breakthrough in apple tree dwarfing through standardization of wide row spacing and small tree spacing has been published online by a team led by Professor Zhenhai Han from the College of Horticulture at China Agricultural University. This research, published in the journal "Nature Genetics," unveils the crucial genetic code behind dwarfing rootstocks for apples, unraveling the mystery of apple dwarfing.
This marks the first time that "Nature Genetics" has published an article in the global fruit tree rootstock research field, laying the theoretical foundation for molecular design breeding of dwarfing rootstocks in woody economic orchards such as apples, and accelerating the realization of a "green revolution."
Rootstocks: The Key to Apple Dwarfing
China is the world's largest producer of apples, accounting for over 56% of global production and more than 40% of the planted area. Currently, "the major challenge facing the healthy and sustainable development of the apple industry is how to deal with the decreasing and aging agricultural labor force, and mechanization and simplification of management are the fundamental solutions," according to Professor Fengwang Ma, chief scientist of the National Apple Industry Technology System and professor at Northwest A&F University, as reported by "Chinese Science News."
Since the 1910s, when the East Malling Research Station in the UK developed the M-series apple dwarfing rootstock, the widespread adoption of dwarfing and dense planting has significantly increased the productivity of apples worldwide, providing effective solutions for the healthy and sustainable development of the apple industry.
Dr. Wei Li, the first author of the paper and associate professor at China Agricultural University, explained that most fruit trees and other economic crops are composite entities of varieties (scions) and rootstocks (underground root systems). The characteristics and interactions of rootstocks and scions determine the growth, development, and yield quality of fruit trees. Dwarfing of fruit trees and other economic crops mainly relies on rootstocks with dwarfing effects, which, when grafted with scion varieties, result in fewer long branches, more short branches, and weakened nutritional growth vigor in the tree.
Therefore, "the key to whether the tree is dwarfed lies in the rootstock; with dwarfing rootstocks, trees can be dwarfed, making them shorter and smaller," said Professor Zhenhai Han, the corresponding author of the paper. Rootstocks are the root system below the grafting interface of fruit trees and other economic crops, playing roles such as providing support, nutrition and water absorption, and secreting organic substances into the rhizosphere soil, thus enhancing the stress resistance and adaptability to local conditions of perennial fruit trees and other economic crops.
Dwarfing and Dense Planting: Standardized Demonstration Orchards for Apple. Image by Wang Xiaoqing.
Introducing dwarfing traits can control the growth vigor of fruit trees and other economic crops, maximizing land use efficiency and increasing yield per unit area to the fullest extent. Widening row spacing maximizes solar energy utilization and significantly improves fruit quality. Tree height is reduced, with some reaching only half or two-thirds of the height of conventionally grown trees. Widened row spacing and consistent spacing between plants in the cultivation system are conducive to mechanical operations, reducing manual labor and making orchard management more convenient and efficient.
"So, the cultivation and cultivation system of dwarfing and dense planting, because of its ability to achieve both economic and ecological benefits, is a trend in the development of global fruit trees and other economic crop production. In the transformation and upgrading of production methods of fruit trees and other economic 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 economic crops, the application on a large scale in production is currently limited to apple orchards and a small number of pear orchards.
Since the 1970s, China has imported dwarfing rootstocks such as M9, M26, B-series, and CG-series from abroad and started breeding work on dwarfing apple rootstocks. 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 dense planting cultivation of Chinese apples from 2% in the early 21st century to nearly 20% now," said Wang Yi, co-corresponding author and professor at China Agricultural University.
"Compared with developed fruit-growing countries, where more than 80% of orchards are dwarfed and densely planted, there is still a big gap. Efficient breeding of dwarfing, multiple resistant rootstocks with strong adaptability to local conditions is of great significance to ensure the healthy and sustainable development of the Chinese apple industry," said Han Zhenhai.
Resource Collection: The Foundation for Deciphering Rootstock Secrets
However, the traditional breeding cycle of apple rootstocks is 20 to 30 years. The deciphering of the dwarfing mechanism of rootstocks and the exploration of key regulatory genes are still in the exploratory stage. The currently published apple genome includes cultivated varieties and a small number of wild relatives such as Gala, Xinjiang wild apple, and forest apple, lacking the genome of apple dwarfing rootstocks. Therefore, "deciphering the genome of apple dwarfing rootstocks is of great value for realizing molecular breeding of apple rootstocks and promoting the modern transformation of apple planting and cultivation patterns," 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 a century, various apple rootstock breeding institutions worldwide have developed numerous clonal rootstock cultivars with different genetic backgrounds, such as the US R series and CG series, the former Soviet Union B series, and China's 'Zhongzhen' series, SH series, and Qingzhen series.
Zhang Hengtao, the co-first author of the paper and a researcher at the Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, told the "Chinese Science Bulletin" that the use of clonal rootstocks is particularly important. Through methods such as tissue culture, cutting, and grafting, clonal rootstocks are propagated without sexual hybridization, ensuring consistent genetic characteristics among offspring, guaranteeing uniform growth, tree shape, yield, and fruit quality, and making orchard management easier, suitable for large-scale production of modern orchards.
Among them, M9 is the most widely used apple dwarfing rootstock globally, 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. "MM106, on the other hand, is a semi-dwarfing rootstock bred by hybridizing M-series rootstocks. Comparing the genomes of M9 and MM106 may reveal candidate genetic variations associated with dwarfing traits," said Han Zhenhai.
Li Hui, co-first author of the paper and a PhD student at China Agricultural University, told the "Chinese Science Bulletin" that to clarify the systematic phylogenetic relationship between different rootstock strains and the genetic background relationship between rootstocks and wild and cultivated species, they collected clonal rootstock materials from apples worldwide.
Since different rootstock strains have different dwarfing, disease resistance, cold tolerance, and drought tolerance characteristics, understanding the systematic phylogenetic relationship and genetic relationship between apple rootstock strains can fully understand and utilize apple genetic resources. It can also help breeders better understand the genetic background differences and genetic variation patterns between different rootstock strains, selectively breed parent plants, improve rootstock breeding efficiency, and provide scientific basis for selecting suitable rootstock strains and rootstock-scion combinations in production.
Based on this, they also constructed a phylogenetic tree and found that apple rootstocks simultaneously accept gene infiltration from wild and cultivated species.
Promoting the Green Revolution in Forestry and Fruit Industry
"Dwarfing rootstocks have already changed the way apples are cultivated, but the genetic basis for inducing dwarfing by dwarfing rootstocks is still not very clear," said Han Zhenhai. In view of this, the team assembled the chromosome-level, nearly complete, and haploid-genotype genomes of the dwarfing rootstock M9, semi-dwarfing rootstock MM106, and Fuji, a common apple cultivar. They successfully discovered an insert sequence that exists only in the M9 genome and further revealed its possible key genetic code for inducing dwarfing in apple rootstocks.
Grafting is a widely used practice in horticulture, and the genetic mechanism behind grafting-induced dwarfing changes in the phenotype of the scion on dwarfing rootstocks remains largely unknown. Previous studies have suggested that large molecules such as mRNA transmitted through vascular tissue between rootstock and scion play an important role in grafting-induced phenotypic changes, but identifying mRNA transfer between rootstock and scion still faces technical challenges.
Title: Advancements in Molecular Breeding for Dwarfing Rootstocks in Fruit Trees
In addressing the issue of dwarfing rootstocks' grafting outcomes, Zhang Hong's team, leveraging the high-quality genome assembly of the Fuji cultivar, developed the bioinformatics pipeline "RNAGlass". This innovative approach identified mRNA transcripts crucially involved in dwarfing, facilitating a comprehensive understanding of the molecular mechanisms behind dwarfing rootstocks.
According to Li Wei, the deciphering of dwarfing genes and their molecular mechanisms in rootstocks paves the way for molecular breeding in the field of woody economic fruit trees, expediting the realization of a "green revolution" by providing a genetic foundation. Breeders can now swiftly screen dwarfing individuals from large-scale materials, eliminating the laborious and time-consuming process of offspring selection in traditional breeding. This not only saves time and resources but also significantly shortens breeding cycles and enhances breeding efficiency.
"It is foreseeable that the traditional 20-30 year breeding cycle for apple rootstocks could be reduced to 10-15 years, facilitating the rapid and efficient breeding of new dwarfing rootstock varieties for apples," said Han Zhenhai. Additionally, dwarfing and high-density planting will propel the fruit industry towards mechanization and intelligence, thereby improving orchard production efficiency and management standards.
However, Han Zhenhai stressed that despite the progress, challenges remain in international apple molecular breeding, including fully exploiting apple's resistance genes and developing transgenic/gene editing technologies for different cultivars.
Meanwhile, there is a growing demand for dwarfing in major fruit trees and other economic crops, particularly in woody fruits and some vigorous-growing species such as pears, peaches, plums, cherries, citrus, chestnuts, and walnuts. The dwarfing genes uncovered in this study exhibit a certain conservatism in controlling plant vigor among fruit trees. Therefore, "this holds the promise of efficient breeding for dwarfing rootstocks in woody economic fruit trees, driving a true green revolution in the fruit industry," said Han Zhenhai.
For more information, refer to the related paper: https://doi.org/10.1038/s41588-024-01657-2
