Data from: The role of Bh4 in parallel evolution of hull color in domesticated and weedy rice

The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de-domestication events, with two genetically distinct weedy rice biotypes in the U.S. derived from the Asian domesticate. One important trait that has been altered by rice domestication and de-domestication is hull color. The wild progenitors of the two cultivated rice species have predominantly black colored hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw colored hulls. Using Black hull 4 (Bh4) as a hull color candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull color variation in the domesticated and weedy rice system. We find that independent Bh4 coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de-domestication.

稻属（Oryza）中独立发生的两次驯化事件分别培育出非洲栽培稻与亚洲栽培稻，为研究趋同演化的遗传基础提供了极具价值的实验体系。该体系同时存在趋同去驯化事件：美国地区存在两种遗传背景迥异的杂草稻生物型，均起源于亚洲栽培稻。谷壳颜色是受水稻驯化与去驯化共同影响的重要性状之一。两个栽培稻物种的野生祖先种谷壳多为黑色，美国两种杂草稻生物型中的一种同样具有黑色谷壳；而两个栽培稻物种与另一种美国杂草稻生物型的谷壳则呈稻草黄色。本研究以黑谷壳4（Black hull 4, Bh4）作为谷壳颜色候选基因，对该基因座的DNA序列变异进行检测，以探究栽培稻与杂草稻体系中谷壳颜色变异的趋同演化机制。研究发现，非洲栽培稻与亚洲栽培稻中独立产生的Bh4编码区突变均与稻草黄色谷壳表型相关，表明该基因正是调控这一趋同性状演化的关键位点。针对美国杂草稻，Bh4单倍型序列验证了当前关于两种杂草稻生物型与亚洲栽培稻之间系统发育关系的假说：稻草黄色谷壳的杂草稻与籼稻（indica）栽培品种亲缘关系最近，而黑色谷壳的杂草稻则与Aus稻（aus）栽培品种亲缘关系最近。选择压力检测结果显示，亚洲栽培稻与稻草黄色谷壳的杂草稻在该基因座上偏离中性进化模式，表明在水稻驯化与去驯化过程中，Bh4均可能受到了定向选择。