柱型苹果MdCoLBD1/2基因生物信息学及SNP分析

柱型苹果(Columnar apple)是苹果株型育种的珍贵资源.利用同源基因克隆方法,以柱型苹果"威塞克旭"一年生枝上休眠期芽cDNA为模板,克隆得到了LOB DOMAIN家族(LBD)的2个同源基因,命名为MdCoLBD1/2,分别编码195和240个氨基酸.该基因有LBD家族的典型结构域,如C盒、GAS盒、亮氨酸拉链(Leu zipper)结构以及LOB Domain区域等.MdCoLBD1/2分别定位于第10条染色体Chr10:18985568..19005801和MdCoLBD2 Chr10:18985594..19005850区间.MdCoLBD1/2与白梨、葡萄、草莓、椰子、梅、核桃的氨基酸的相似性均在60%以上.聚类分析表明MdCoLBD1和白梨、梅、草莓亲缘关系较近,MdCoLBD2与葡萄、核桃亲缘关系较近,MdCoLBD1/2与亚洲棉、陆地棉的聚类关系均较远.通过测序分析了MdCoLBD1/2基因在30个不同类型材料中的碱基序列差异,得到MdCoLBD1有8个碱基差异位点,MdCoLBD2有5个碱基差异位点.

Bioinformatics and SNP Analysis of MdCoLBD1/2 Genes on Columnar Apple

The columnar apple is a precious resource for the apple breeding of plant architecture.The dormant buds cDNA of one-year-old branches from columnar apple"Wijcik McIntosh" were used as experimental materials for cloning LOB DOMAIN(LBD) two genes by homologous gene cloning method, which were named MdCoLBD1/2, encoding 195 and 240 amino acids respectively.MdCoLBD1/2 genes have the typical Domain of LBD family, such as C block, GAS block, leucine zipper (Leu zipper) structure and LOB Domain, etc.By genetic mapping, MdCoLBD1/2 located in the linkage group-10 Chr10:18985568..19005801 and Chr10:19005801..19005850 respectively.The identity of amino acid between MdCoLBD1/2 and other LBD genes from white pear, grapes, strawberries, coconut, plum, walnut are more than 60%.The phylogenetic tree of LBD family showed that MdCoLBD1 was more close with LBD genes from white pear, plum and strawberry, MdCoLBD2 was more close with grapes, walnuts, and MdCoLBD1/2 were all far away from asiatic cotton and upland cotton.Using sequencing method to analyze the sequence different of MdCoLBD1/2 in different plant architecture material, the results showed that the MdCoLBD1 gene has 8 nucleotide differences sites, the MdCoLBD2 gene has 5 nucleotide differences sites.