鲤品种间生长性状共享与特异QTL的遗传机制

Marker-assisted selection is the developing direction for cultured fish breeding. Therefore, detection of markers and genes closely linked to important economic traits has been the main research frontier for genetic breeder in recent two decades. Although substantial significant QTL and markers have been obtained for cultured fish, few of them was successfully used for breeding due to their differences among various populations. What are the genetic factors of the major QTL variations in different populations of the same species? What are the genetic mechanisms for the shared QTL among various varieties or families? What role do the key genes in the shared and specific QTL regions play in the variations among different varieties? To resolve the scientific and technical problems of the main effect of QTL variation, we propose to analyze the shared and specific QTL regions affecting growth traits between mirror carp (Cyprinus carpio L.) and jian carp (C. c. var. jian) obtained in previous studies. At first, the candidate genes in the QTL regions will be screened out by aligning QTL sequences to the reference genome of common carp. Secondly, these candidate genes and associated markers will be verified by correlation analysis between gene expressive quantity by real time fluorescence quantitative PCR and individual genotypes of large amount of samples and growth traits, respectively. Finally, comparative genomic analysis will be carried out between zebrafish and common carp. The aim of this study is to elucidate the structures and functions of the key genes in QTL regions and reveal the genetic mechanism of the variations for the significant QTL.

标记辅助选择是养殖鱼类育种的发展方向，鉴定重要经济性状紧密连锁的标记/基因是近二十年遗传育种学家的主要研究工作。尽管养殖鱼类已获得相当多的主效QTL和标记，但在育种上成功应用的例子并不多，关键问题之一是主效QTL变异较大。同一物种的主效QTL在群体间变异大的遗传因素是什么？品种间和家系间共享QTL的遗传机制是什么？QTL区间内的关键基因在品种间共享和特异的变化中起什么作用？针对主效QTL经常发生变异、难以解析的科学与技术难题，本项目以前期获得的两个鲤(Cyprinus carpio)品种镜鲤与建鲤在生长性状上的共享QTL和变异QTL为研究对象，比对鲤的参考基因组筛查出QTL区间内的候选基因，通过分析基因表达量及大群体样本基因型与性状的关联性来验证候选基因及连锁标记，进而借助与斑马鱼等模式生物的比较基因组分析，最终阐明QTL区间关键基因的结构和功能，以此破解主效QTL经常发生变异的遗传机制。

本研究针对经济性状的主效QTL在不同群体间经常发生变异的科学问题，以鲤(Cyprinus carpio)品种间生长性状共享与特异QTL区间为研究对象，(1)依据鲤高密度遗传图谱和参考基因组，确定了QTL区间的功能基因及其特征，发现共享QTL区间内调控生长和发育的基因(36.66%)显著多于特异QTL(22.34%)，推测具有更多的调控生长和发育的功能基因可能是QTL在群体间稳定和共享的遗传基础，并从中筛选生长性状的候选基因30个，主要位于代谢、TGF-β以及IGF信号通路，用同池饲养的最大组与最小组对其中10个候选基因进行了qPCR分析和验证。(2)对镜鲤(MM)、建鲤(JJ)和黄河鲤(HH)幼鱼期的最大组和最小组脑、肝脏和肌肉进行转录组分析，分别获得195个、156个和953个差异表达基因，只有1个基因为3个鲤品种共享，JJ与HH共享差异表达基因最多(43个)，MM与HH其次(17个)，MM与JJ最少(3个)，表明不同鲤品种的差异表达基因也不同，共享差异表达基因的多少与遗传背景相关，即生长相关基因的表达量在品种间差异很大，只有少数共享基因具有相同或相似的表达趋势，从中筛选出一批生长性状的候选基因。(3)用3个鲤品种多家系样本对前期获得的28个QTL进行验证，在6月龄和18月龄样本中分别获得9个和2个共享QTL标记；在两个规格样本的比较中，分别获得了9个(MM)、3个(JJ)和22个(HH)共享QTL标记，结果表明以现有遗传资源为基础进行不同群体共享QTL标记的筛选是可行而高效的，但是群体的特异QTL标记仍然占多数。研究结果从QTL标记、差异表达基因以及候选基因表达量3个角度比较了品种间数量性状座位及基因的变动，加深了对群体间QTL变异的理解和认识，为进一步阐明QTL变动的遗传机制奠定了基础。