Isolation and characterization of the barley gene controlling hulled or naked caryopsis

在大麦中，去壳颖果或裸颖果性状是重要的农艺性状之一，因为它与收获的大麦籽粒作为麦芽/饲料用途或人类食物的效用密切相关。我们尝试用定位克隆方法分离和鉴定大麦壳颖果或裸颖果的控制基因。首先，我们利用AFLP和散装分离分析开发了连锁分子标记。对假定的AFLP连锁带进行测序，以建立基于PCR的标记。然后，对大型分离群体进行分析，以获得该基因的精细定位。这种定位导致基因两侧有两个共显性标记，遗传距离近端分别为0.6 cM和远端分别为0.06 cM。接下来，利用生物信息学方法鉴定大麦基因组和水稻基因组中裸颖果基因的微共生性。我们成功地鉴定出与水稻6号染色体长臂的微共线性。利用水稻基因组序列信息有效地进一步缩小了大麦基因组中裸颖果基因的范围。然后我们开始构建整个轨迹的物理地图。我们成功构建了约500kb的大麦BAC序列，该序列横跨有壳颖果基因和裸颖果基因。在现有资料的基础上，我们确定了一个大麦去壳颖果或裸颖果性状的候选基因。表达分析似乎支持该基因的身份。我们还分析了诱导的裸颖果突变体，发现了非同义突变，这巩固了我们的结论。我们得出结论，世界上的裸大麦有一个单一的起源，似乎发生在中东。基于裸颖果基因分子标记的等位基因变异，我们阐明了裸大麦在东亚的两条独立迁徙路线。

In barley, the hulled or naked caryopsis trait is one of essential agronomic characters because it is closely associated with the utility of harvested barley grains either as malting/feeding purpose or human food.. We attempted isolation and characterization of the barley gene controlling hulled or naked caryopsis using a positional cloning approach. First, we developed linked molecular markers by using AFLP and bulked segregant analysis. Putative linked AFLP bands were sequenced to develop PCR based markers. Then, large segregating populations were analyzed for a fine mapping of the gene. This mapping resulted in the state where the gene was flanked by two co-dominant markers with genetic distance of 0.6 cM in proximal side and 0.06 cM in distal side, respectively. Next, bioinformatics were applied to identify microsynteny between the naked caryopsis gene in the barley genome and the rice genome. We successfully identified microcollinearity with the long arm of rice chromosome 6. Rice genome sequence information was effectively used to further narrow down the naked caryopsis gene in the barley genome. We then started the physical map construction of the entire locus. We have successfully constructed the barley BAC contig of about 500 kb, which spans the hulled or naked caryopsis gene. On the bases of available information, we have identified a candidate gene for the hulled or naked caryopsis character in barley. Expression analysis seems to support the identity of this gene. We also analyzed induced naked caryopsis mutants and found non-synonymous mutations, which solidified our conclusion. We conclude that naked barley in the world has a single origin, which appears to have occurred in the Middle East. On the basis of allelic variation of a molecular marker that was tightly linked to the naked caryopsis gene, we elucidated two independent migratory routes of naked barley into East Asia.