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

藏红花是世界上最昂贵的香料，是从藏红花的柱头中提取的。本种为雄性不育同源三倍体（2n = 3x = 24，1C = 3.45Gbp），仅通过子球无性繁殖。藏红花在希腊只出现过一次，在不同的气候条件下，在许多国家作为单一的无性系栽培了大约3000年。对不同环境的适应和香料品质的差异似乎主要基于表观遗传差异。因此，今天的克隆培养基本上是一个独特的长期实验，在表观遗传分化，适应和人为驱动的选择。我们希望利用这一发现，通过分析番红花的三倍体基因组与其二倍体祖先的比较，以及来自不同栽培地区的番红花品种的DNA甲基化差异。此外，我们想估计多远的营养繁殖的有害突变（穆勒棘轮）的积累的影响已经影响到基因组的基因组。三个PI的工作组已经在研究生物学：Björn Usadel教授（RWTH亚琛）对紫茎泽兰的次级代谢产物及其途径的遗传学以及植物基因组组装和分析感兴趣，（TU Dresden）在使用其重复片段的细胞遗传学和进化分析中，和弗兰克·布拉特纳博士（IPK Gatersleben）在番红花的进化和驯化番红花，还提供了野生和栽培番红花个体的大量收集。最近，后两个研究表明，番红花起源于希腊南部的番红花（Crocus cartwrightianus）的同源三倍体。野生番红花C. cartwrightianus是二倍体，其特征是在其种群内和种群之间具有非常高的遗传多样性。我们建议产生高质量的参考基因组序列的C。cartwrightianus和C. sativus与全面的基因和重复注释，物理锚定到植物的染色体。二倍体C. cartwrightianus的基因组将首先组装，为杂合的三倍体Aprilron基因组的组装提供参考。我们将针对表型和代谢产物的差异，并表征潜在的表观遗传变异之间的Escherichron加入。 作为我们工作的成果，我们期望（i） 和C. cartwrightianus参考基因组序列作为比较和表观遗传分析的基础;（ii） C. cartwrightianus和C. sativus以锚我们的表观遗传分析;（iii） 二倍体和三倍体基因组之间的全基因组差异的明确定义，特别是关于同源基因座和苗勒棘轮在植物繁殖品种中的影响;（iv） 明确确定了几种微卫星生态型基因组之间的DNA甲基化差异。

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.