Olsen Kenneth M, Halldorsdottir Solveig S, Stinchcombe John R, Weinig Cynthia, Schmitt Johanna, Purugganan Michael D
Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA.
Genetics. 2004 Jul;167(3):1361-9. doi: 10.1534/genetics.103.024950.
The selfing plant Arabidopsis thaliana has been proposed to be well suited for linkage disequilibrium (LD) mapping as a means of identifying genes underlying natural trait variation. Here we apply LD mapping to examine haplotype variation in the genomic region of the photoperiod receptor CRYPTOCHROME2 and associated flowering time variation. CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene; in addition, a haplotype possessing a radical glutamine-to-serine replacement (AS) occurs within the more common haplogroup. Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering. Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2. Whereas the B haplogroup cannot be delimited to <16 kb around CRY2, the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype. This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
自花授粉植物拟南芥被认为非常适合用于连锁不平衡（LD）作图，以此来鉴定自然性状变异背后的基因。在此，我们应用LD作图来研究光周期受体隐花色素2（CRY2）基因组区域的单倍型变异以及相关的开花时间变异。CRY2的DNA序列显示出强烈的LD，并且在整个基因中存在两个高度分化的单倍型类群（A和B）；此外，在更常见的单倍型类群中出现了一种具有从谷氨酰胺到丝氨酸的根本替换（AS）的单倍型。使用由95个生态型组成的未分层群体进行的生长室和田间实验表明，在短日照光周期条件下，AS和B单倍型类群均与早花高度显著相关。来自CRY2侧翼六个基因的数据表明，这些单倍型类群局限于CRY2周围大约65 kb的基因组区域。虽然B单倍型类群不能限定在CRY2周围小于16 kb的区域内，但AS单倍型类群几乎完全由与CRY2中丝氨酸替换直接相关的核苷酸多态性所表征；这一发现强烈表明丝氨酸替换直接导致了AS早花表型。这项研究证明了LD作图在阐明拟南芥中自然的、与生态相关的变异的遗传基础方面的效用。
