Quantitative trait locus mapping reveals an independent genetic basis for joint divergence in leaf function, life-history, and floral traits between scarlet monkeyflower (Mimulus cardinalis) populations

AbstractPREMISE Across taxa, vegetative and floral traits that vary along a fast-slow life-history axis are often correlated with leaf functional traits arrayed along the leaf economics spectrum, suggesting a constrained set of adaptive trait combinations. Such broad-scale convergence may arise from genetic constraints imposed by pleiotropy (or tight linkage) within species, or from natural selection alone. Understanding the genetic basis of trait syndromes and their components is key to distinguishing these alternatives and predicting evolution in novel environments. METHODS We used a line-cross approach and quantitative trait locus (QTL) mapping to characterize the genetic basis of twenty leaf functional/physiological, life history, and floral traits in hybrids between annualized and perennial populations of scarlet monkeyflower (Mimulus cardinalis). RESULTS We mapped both single and multi-trait QTLs for life history, leaf function and reproductive traits, but found no evidence of genetic co-ordination across categories. A major QTL for three leaf functional traits (thickness, photosynthetic rate, and stomatal resistance) suggests that a simple shift in leaf anatomy may be key to adaptation to seasonally dry habitats. CONCLUSIONS Our results suggest that the co-ordination of resource-acquisitive leaf physiological traits with a fast life history and more selfing mating system results from environmental selection rather than functional or genetic constraint. Independent assortment of distinct trait modules, as well as a simple genetic basis to leaf physiological traits associated with drought escape, may facilitate adaptation to changing climates. , MethodsThe spreadsheet contains four sheets.  1. phenotypic data for all individuals in the experiment (including parents and F1 hybrids and all f2s hybrid) used for calculation of quantiative genetic summaries (heritability, genetic covariances). Both raw values and standardized values (see methods) are included. 2. phenotype matrix for the subset of F2 hybrids used for genetic mapping.  3. genotype matrix for the subset of F2 hybrids used for genetic mapping, coded as CC for CE10 homozygote, CW for heterozygote and WW for WFM homozygote. 4.  genetic map of markers used for QTL mapping (marker numbers are not meaningful but match those in the genotype matrix) Both phenotypes and genotypes are not raw data. Phenotypic values such as relative growth rate, assimilation rate, or leaf thickness were calculated, as described in the Methods text, from underlying measurements. The called genotypes are derived from gene-capture sequence data available on the Sequence Read Archive, using the protocols described in the text. The authors are willing to share the raw phenotypic data (e.g. leaf area) by request. We can privately provide spreadsheets that match markers to physical map positions., Usage notesThere are missing genotypes and phenotypes for some individuals (indicated by NA or - in the cell).  Genetic correlations were calculated using individuals without missing data for any trait. The three F2 files are in rQTL2 input format.

【摘要与前提】
在各类生物类群中，沿快慢生活史轴变异的营养与花部性状，通常与沿叶片经济谱(leaf economics spectrum)排布的叶片功能性状呈显著相关，这表明适应性性状组合存在约束范围。这种大尺度的趋同演化现象，可能源于物种内多效性(pleiotropy)或紧密连锁带来的遗传约束，也可能仅由自然选择驱动。解析性状综合征及其组分的遗传基础，是区分这两种演化机制、预测新环境下物种演化的关键。

【研究方法】
本研究采用杂交系方法与数量性状位点(QTL)定位技术，对一年生与多年生猩红色沟酸浆(Mimulus cardinalis)种群间杂交后代的20项叶片功能/生理、生活史及花部性状的遗传基础进行了表征。

【研究结果】
我们定位了生活史、叶片功能与繁殖性状的单性状及多性状QTL，但未发现不同类别性状间存在遗传协同的证据。针对三项叶片功能性状(叶片厚度、光合速率与气孔阻力)的主效QTL表明，叶片解剖结构的简单改变可能是物种适应季节性干旱生境的关键。

【研究结论】
本研究结果显示，资源获取型叶片生理性状与快速生活史及更高度自交交配系统的协同演化，源于环境选择而非功能或遗传约束。不同性状模块的独立分配，以及与干旱逃逸相关的叶片生理性状的简单遗传基础，可能促进了物种对气候变化的适应。

【数据集说明】
本研究配套电子表格包含4个工作表：
1. 实验所有个体(包括亲本、F1杂交种及全部F2杂交个体)的表型数据，用于计算定量遗传统计量(遗传力、遗传协方差)，包含原始值与标准化值(详见研究方法部分)。
2. 用于遗传定位的F2杂交亚群的表型矩阵。
3. 用于遗传定位的F2杂交亚群的基因型矩阵，编码规则为：CC代表CE10纯合子，CW代表杂合子，WW代表WFM纯合子。
4. 用于QTL定位的标记遗传图谱(标记编号无实际意义，但与基因型矩阵中的标记一一对应)。
注：表型与基因型数据均非原始测量数据。相对生长速率、光合速率、叶片厚度等表型值，均根据研究方法部分描述的流程由原始测量数据计算得到。已标注的基因型源自基因捕获测序数据，该数据可在序列读取档案(Sequence Read Archive)中获取，分析流程详见原文。作者可应要求共享原始表型数据(如叶面积数据)，亦可私下提供标记与物理图谱位置匹配的电子表格。

【使用说明】
部分个体存在基因型与表型缺失值(单元格中以NA或-表示)。遗传相关性计算仅使用无任何性状缺失数据的个体。三个F2相关文件均为rQTL2软件的输入格式。