破解铁观音基因组，找到茶叶高产“开关”

　科学家成功破解了中国名茶铁观音的基因组，还对161个茶树品种和15个近缘种大理茶进行了重测序分析，发现了影响植株高矮和茶叶产量的两个功能基因。

　　茶树是世界重要的饮料作物，然而其滞后的基因组学研究，限制了利用分子生物学技术对其进行优良性状的快速选育，如今这一窘境有望被打破。

　　记者7月25日从福建农林大学获悉，该校尤民生教授和中国农科院深圳农业基因组研究所张兴坦研究员，联合国内外多家单位的科学家，成功破解了中国名茶铁观音的基因组，相关成果近日发表在国际顶级期刊《自然·遗传学》上。

　　“研究成果阐述了等位基因在长期无性繁殖过程中应对‘遗传负荷’的机制和茶树的群体演化、驯化史。特别是，我们发现的两个功能基因，极有可能为茶树植株矮化、产量提高作出贡献。”尤民生告诉记者。

破译基因组

弄清茶树应对“遗传负荷”秘密

　　许多重要作物都是无性繁殖，例如茶树、马铃薯和木薯等。无性繁殖可以有效保留亲本优良基因型，有利于快速筛选和培育新品种。然而这种繁殖方式容易使作物缺乏遗传多样性，从而导致作物更易遭受害虫和病原菌等有害生物的侵袭，并易积累大量的有害突变，致使农作物对有害生物的抗性和适应环境的能力降低，直接影响重要农艺性状。“因此，解析无性繁殖作物的基因组信息，对于及时鉴定和清除有害突变，改善作物的抗性和品质至关重要。”尤民生说。

　　研究选取的基因组测序对象“铁观音”是中国十大名茶之一，因茶树自交不亲和、种间频繁杂交等因素，导致其基因组高度杂合、组装难度很大。该团队利用最新技术攻克了高杂合基因组组装难题，成功获得了两个铁观音基因组——单倍体参考基因组和单倍体分型基因组。结果显示，来自父母本的两套单倍型之间存在大量遗传变异。

　　铁观音距今已有约300年的栽培历史，长期的无性繁殖积累大量体细胞突变（包括有害突变），增加了遗传负荷，导致其适应性降低。然而，人们对无性繁殖作物如何应对遗传负荷这一问题知之甚少。

　　传统的杂种优势现象可以由显性效应和超显性效应两种假说解释：显性效应指个体倾向于利用有利于生长和发育的优势等位基因（或显性基因）而忽略对个体不利的劣势基因（或隐形基因）；超显性效应指杂合等位组合在多种生境下优于任一纯合等位的现象。

　　研究结果显示，在无性繁殖的茶树基因组中，显性效应可能是其应对遗传负荷的重要机制。面对大量积累的体细胞突变或有害突变，长期无性繁殖的茶树利用优势等位基因，来应答不断积累的遗传负荷，以维持其正常的生长发育和对环境的适应性。

揭示关键基因

有望实现植株矮化、产量提高

　　该团队在攻克铁观音基因组的基础上，通过对茶树种群水平的遗传分析，揭示了该物种的演化和人工驯化历史。研究人员对161个茶树品种和15个近缘种大理茶进行重测序分析发现，各茶区存在频繁的种质基因交流，其中一些与有记录的茶树杂交育种历史相吻合。证据表明，茶树与近缘种间频繁的杂交渐渗是其网状演化和维持茶树遗传多样性的重要因素。此外，人们对大叶茶和小叶茶制品的偏爱有所不同也导致了两者经历了平行的驯化历程。

　　“该研究成果也为利用组学分析和分子生物学技术挖掘功能基因、解析其背后的遗传调控机制、开展基因组设计育种，奠定了坚实的理论基础。”张兴坦说。

　　原来20世纪60年代，大规模推广矮秆或半矮秆的水稻和小麦品种极大地提高了作物产量，其中控制株高的水稻sd1基因和小麦rht基因，也因其巨大的贡献被称为“绿色革命基因”。研究人员发现，茶树的株高在长期的栽培过程中也受到了驯化，体现在两个细胞色素P450家族基因（CsDWF4和CsBAS1）受到人工选择。这两个基因是油菜素内酯生物合成的关键基因，参与植物的光形态建成。

　　“这两个基因或能调节植株高矮、茶叶产量。”尤民生表示，在接下来的研究中，他们将利用组学分析和分子生物学技术进一步挖掘两个基因的功能，积极开展基于大数据驱动的基因组设计育种探索，有效缩短优质茶树品种育种周期、提高育种效率、降低育种成本。

Scientists have successfully deciphered the genome of Tieguanyin, a famous Chinese tea. They also performed resequencing analysis on 161 tea varieties and 15 closely related Dali teas, and found two functional genes that affect plant height and tea yield.

Tea tree is an important beverage crop in the world. However, its lagging genomics research limits the rapid selection of its excellent traits using molecular biology techniques. Now this dilemma is expected to be broken.

The reporter learned from Fujian Agriculture and Forestry University on July 25 that Professor You Minsheng of the school and researcher Zhang Xingtan of the Shenzhen Institute of Agricultural Genomics, Chinese Academy of Agricultural Sciences, together with scientists from many domestic and foreign units, successfully cracked the genome of the famous Chinese tea Tieguanyin, and related achievements Recently published in the top international journal "Nature Genetics".

"The research results illustrate the mechanism by which alleles respond to 'genetic load' during long-term asexual reproduction and the population evolution and domestication history of tea plants. In particular, the two functional genes we discovered are very likely to contribute to dwarfing, Contribute to the increase in production." You Minsheng told reporters.

Decipher the genome

Unravel the secrets of tea tree coping with 'genetic load'

Many important crops are vegetatively propagated, such as tea tree, potato and cassava. Asexual reproduction can effectively retain the superior genotypes of the parents, which is conducive to the rapid screening and breeding of new varieties. However, this way of reproduction tends to make crops lack genetic diversity, which makes crops more vulnerable to pests and pathogens and other harmful organisms, and easily accumulates a large number of harmful mutations, resulting in reduced resistance of crops to harmful organisms and reduced ability to adapt to the environment. Directly affects important agronomic traits. "Therefore, analyzing the genomic information of vegetatively propagated crops is crucial for timely identification and removal of harmful mutations and improvement of crop resistance and quality." You Minsheng said.

The genome sequencing target "Tieguanyin" selected for the study is one of the top ten famous teas in China. Due to factors such as self-incompatibility and frequent interspecific hybridization, its genome is highly heterozygous and difficult to assemble. The team used the latest technology to overcome the high heterozygous genome assembly problem, and successfully obtained two Tieguanyin genomes—a haploid reference genome and a haplotyped genome. The results showed that there was a large amount of genetic variation between the two sets of haplotypes from the parents.

Tieguanyin has been cultivated for about 300 years. Long-term asexual reproduction accumulated a large number of somatic mutations (including harmful mutations), which increased the genetic load and reduced its adaptability. However, little is known about how vegetatively propagated crops respond to genetic load.

The traditional heterosis phenomenon can be explained by two hypotheses: dominant effect and superdominant effect: dominant effect refers to the tendency of individuals to use the dominant allele (or dominant gene) that is beneficial to growth and development and ignore the unfavorable alleles. A disadvantaged gene (or recessive gene); a superdominant effect refers to the phenomenon in which a combination of heterozygous alleles is superior to any homozygous allele in multiple habitats.

The results show that in the genome of asexually propagated tea plants, the dominant effect may be an important mechanism for coping with genetic load. Facing a large accumulation of somatic mutations or deleterious mutations, long-term asexually propagated tea plants use dominant alleles to respond to the accumulated genetic load to maintain their normal growth and development and adaptability to the environment.

Revealing key genes

Potential for dwarfing plants and increasing yields

On the basis of conquering the Tieguanyin genome, the team revealed the evolution and artificial domestication history of the species through genetic analysis at the population level of the tea tree. The resequencing analysis of 161 tea plant varieties and 15 closely related species Dali tea found that there were frequent germplasm gene exchanges in each tea area, some of which were consistent with the recorded history of tea cross-breeding. Evidence suggests that frequent hybrid introgression between tea plants and related species is an important factor in their network evolution and maintenance of tea genetic diversity. In addition, people's preferences for large-leaf tea and small-leaf tea products have also led to parallel domestication processes.

"The research results have also laid a solid theoretical foundation for using omics analysis and molecular biology techniques to mine functional genes, analyze the genetic regulation mechanism behind them, and carry out genome design breeding." Zhang Xingtan said.

It turned out that in the 1960s, the large-scale promotion of dwarf or semi-dwarf rice and wheat varieties greatly improved crop yield, among which the rice sd1 gene and wheat rht gene, which control plant height, are also known as "" Green Revolution Gene". The researchers found that the plant height of tea trees has also been domesticated during the long-term cultivation process, which is reflected in the artificial selection of two cytochrome P450 family genes (CsDWF4 and CsBAS1). These two genes are key genes in brassinolide biosynthesis and are involved in photomorphogenesis in plants.

"These two genes may be able to regulate plant height and tea yield." You Minsheng said that in the next research, they will use omics analysis and molecular biology technology to further explore the functions of the two genes, and actively carry out research based on big data. Driven genome design breeding exploration can effectively shorten the breeding cycle of high-quality tea varieties, improve breeding efficiency, and reduce breeding costs.