Identical genomes but different properties – saffron as a model for epigenetics of quality traits and environmental adaptation

相同的基因组但不同的特性——藏红花作为品质性状和环境适应表观遗传学的模型

• 批准号: 433081887
• 负责人: Dr. Frank R. Blattner
• 金额: --
• 依托单位: Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/433081887?language=en
• 关键词: Identical; genomes; but; different; properties

Saffron, the most expensive spice of the world, is produced from the stigmas of the saffron crocus, Crocus sativus. This species is a male sterile autotriploid (2n = 3x = 24, 1C = 3.45 Gbp), propagated only vegetatively through daughter corms. Saffron crocus emerged only once in Greece, and was cultivated for about 3000 years as a single clonal lineage in many countries under different climate conditions. Adaptation to different environments and spice quality differences seem mainly based on epigenetic differences. Thus, today’s saffron cultivation is essentially a unique long-term experiment in epigenetic differentiation, adaptation, and human-driven selection. We want to take advantage of this finding by analyzing the triploid genome of saffron crocus in comparison to its diploid progenitor and the differences in DNA methylation of saffron cultivars from diverse cultivation areas. Moreover, we want to estimate how far the effects of vegetative propagation regarding the accumulation of detrimental mutations (Muller’s ratchet) are already influencing the genome of saffron. The working groups of the three PIs already work on saffron biology: Prof. Björn Usadel (RWTH Aachen) is interested in saffron’s secondary metabolites and the genetics of their pathways as well as plant genome assembly and analysis, Dr. Tony Heitkam (TU Dresden) in the cytogenetic and evolutionary analysis of saffron using its repeat fraction, and Dr. Frank Blattner (IPK Gatersleben) in the evolution of Crocus and domestication of saffron, also providing a large collection of wild and cultivated Crocus individuals. Very recently, the latter two showed that saffron originated as an autotriploid from Crocus cartwrightianus in southern Greece. In contrast to saffron crocus, wild C. cartwrightianus is diploid, and characterized by very high genetic diversity within and among its populations. We propose to generate high quality reference genome sequences for C. cartwrightianus and C. sativus with comprehensive gene and repeat annotations, physically anchored to the plants’ chromosomes. The diploid C. cartwrightianus genome will be assembled first, providing a reference for the assembly of the heterozygous triploid saffron genome. We will target the differences in phenotypes and metabolites, and characterize the underlying epigenetic variation between saffron accessions. As outcome of our work we expect (i) the saffron and C. cartwrightianus reference genome sequences as the basis for comparative and epigenetic analysis; (ii) the annotated gene and repeat fractions of C. cartwrightianus and C. sativus to anchor our epigenetic analysis; (iii) a clear definition of genome-wide differences between the di- and triploid genomes, particularly with respect to homoeologous loci and the effects of Muller’s ratchet in the vegetatively propagated cultivars; (iv) the clear determination of DNA methylation differences between the genomes of several saffron ecotypes.

藏红花是世界上最昂贵的香料，由藏红花藏红花的柱头制成。本种是雄性不育的同源三倍体(2n=3x=24，1C=3.45 GBP)，只通过子球茎营养繁殖。藏红花只在希腊出现过一次，并在不同的气候条件下作为单一克隆血统在许多国家种植了约3000年。对不同环境的适应和香料品质的差异似乎主要是基于表观遗传差异。因此，今天的藏红花栽培本质上是在表观遗传分化、适应和人类驱动的选择方面进行的独特的长期实验。我们想利用这一发现，通过分析藏红花的三倍体基因组与其二倍体祖先的比较，以及不同栽培地区藏红花品种DNA甲基化的差异来加以利用。此外，我们想要估计营养繁殖对有害突变(穆勒棘轮)积累的影响已经在多大程度上影响藏红花的基因组。这三个PI的工作组已经在研究藏红花生物学：Björn Usadel教授(RWTH Aachen)对藏红花次生代谢物及其途径的遗传学以及植物基因组组装和分析感兴趣，Tony Heitkam博士(德累斯顿理工学院)研究藏红花的细胞遗传学和进化，利用其重复片段对藏红花进行细胞遗传学和进化分析，Frank Blattner博士(IPK Gatersleben)研究藏红花的进化和驯化藏红花，这也提供了大量藏红花野生和栽培个体的集合。最近，后两项研究表明，藏红花起源于希腊南部的西红花，是一种同源三倍体。与藏红花不同的是，野生卡特鲁蒂安是二倍体，其种群内和种群之间具有非常高的遗传多样性。我们建议用物理上固定在植物染色体上的全面基因和重复注释来生成高质量的Cartwright tianus和Cativus的参考基因组序列。将首先组装二倍体红花藏红花基因组，为杂合三倍体藏红花基因组组装提供参考。我们将针对表型和代谢物的差异，并表征藏红花材料之间潜在的表观遗传差异。作为我们工作的结果，我们期望(I)藏红花和C.cartwright tianus参考基因组序列作为比较和表观遗传分析的基础；(Ii)Cartwright tianus和C.cartwright tianus的注释基因和重复片段用于我们的表观遗传学分析；(Iii)明确定义二倍体和三倍体基因组之间的差异，特别是关于同源位置和Muller棘轮在无性繁殖品种中的影响；(Iv)明确测定几个藏红花生态型基因组之间的DNA甲基化差异。