Transcription factors and molecular markers revealed asymmetric contributions between allotetraploid Upland cotton and its two diploid ancestors

ABSTRACT Three Gossypium species have been used to breed cotton as they vary in their fiber production and resistance to stresses. Transcription factors (TFs) mostly are present in different copies or isoforms by which they conduct their regulation. Their copy number can determine organism behavior to a cue. Simple sequence repeats (SSRs) are one of the most informative and versatile molecular markers. Transcription factors of three Gossypium species were compared in silico. Seventy eight percent of TFs were common between the three species. Single copy for each species were 6057 TF. Gossypium hirsutum and G. raimondii shared the most common interspecific TF. Gossypium arboreum species-specific TF were the least. MYB TF family with its subfamilies is the most abundant followed by bHLH and AP2/ERF family. Gossypium hirsutum generally possesses more TF copies compared to other two species. The 2109 single-copy clusters indicate that G. hirsutum has received one copy from only one parent. The five most abundant SSR markers of TF were dinucleotides AT, TA, TC, CT and TG belonging to G. raimondii. For G. arboreum and G. hirsutum they were trinucleotides CAA, CGA, TGA, GAA (CAT: G. hirsutum) and TCA. The findings suggest that there is regulatory difference between the three Gossypium species for fiber production and insect attack response. The differences may be due to some adaptive deletion events during speciation of G. hirsutum from its parents G. arboreum and G. raimondii.

摘要 鉴于三种棉属（Gossypium）物种在纤维产量与抗逆性方面存在差异，其被广泛应用于棉花育种工作。转录因子（Transcription factors，TFs）大多以不同拷贝或同工型的形式存在，并借此发挥调控功能，而其拷贝数可决定生物体对信号的响应行为。简单序列重复（Simple sequence repeats，SSRs）是目前信息含量最丰富、应用最广泛的分子标记之一。本研究通过计算机模拟（in silico）方法对三种棉属物种的转录因子进行了比较分析。结果显示，三种物种中共有的转录因子占比达78%，各物种的单拷贝转录因子数量均为6057个。陆地棉（Gossypium hirsutum）与雷蒙德氏棉（G. raimondii）共享的种间转录因子数量最多，亚洲棉（Gossypium arboreum）的物种特异性转录因子数量最少。MYB转录因子家族及其亚家族的丰度最高，其次为bHLH家族与AP2/ERF家族。相较于另外两个物种，陆地棉的转录因子拷贝数整体更多。2109个单拷贝基因簇表明，陆地棉仅从单一亲本处获得了一个拷贝。雷蒙德氏棉中转录因子相关的5种丰度最高的SSR标记为二核苷酸重复序列AT、TA、TC、CT与TG；亚洲棉与陆地棉的对应丰度最高SSR标记则为三核苷酸重复序列CAA、CGA、TGA、GAA（陆地棉为CAT）与TCA。研究结果表明，三种棉属物种在纤维产量与虫害响应方面存在调控差异，此类差异可能源于陆地棉由亚洲棉与雷蒙德氏棉两个亲本物种形成过程中发生的适应性缺失事件。