Abstract
Picea crassifolia Kom. is one of the timber and ecological conifers in China and its wood tracheid traits directly affect wood formation and adaptability under harsh environment. Molecular studies on P. crassifolia remain inadequate because relatively few genes have been associated with these traits. To identify markers and candidate genes that can potentially be used for genetic improvement of wood tracheid traits, we examined 106 clones of P. crassifolia, and investigated phenotypic data for 14 wood tracheid traits before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the studied traits. We developed 4,058,883 SLAF-tags and 12,275,765 SNP loci, and our analyses identified a total of 96 SNP loci that showed significant correlations with three earlywood tracheid traits using a mixed linear model (MLM). Next, candidate genes were screened in the 100 kb zone (50 kb upstream, 50 kb downstream) of each of the SNP loci, whereby 67 candidate genes were obtained in earlywood tracheid traits, including 34 genes of known function and 33 genes of unknown function. We provide the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in wood traits improvement and candidate genes for the development of earlywood tracheid in P. crassifolia.
Highlights
Picea crassifolia Kom. (Qinghai spruce) is an evergreen conifer native to the Qilian Mountain areas of northwestern China that are known to be among the world’s arid and semi-arid mountains
A total of 67 highly significant single nucleotide polymorphism (SNP) loci were associated with three earlywood tracheid traits, ELDR, EWLR, and EWT
These SNP loci have identified a set of candidate genes that could be exploited to improve earlywood tracheid traits for regulating development of earlywood tracheid for ecological adaptability of P. crassifolia under arid and semi-arid conditions
Summary
Picea crassifolia Kom. (Qinghai spruce) is an evergreen conifer native to the Qilian Mountain areas of northwestern China that are known to be among the world’s arid and semi-arid mountains. Drought is the primary factor for limiting tree growth in arid and semi-arid regions, greatly influencing xylem anatomical traits [4]. Studies conducted on P. crassifolia sampled from different altitudes of the Tibetan plateau, northwestern China, found that the development of tracheid radial diameter is closely related to temperature and precipitation, and trees could change their internal characteristics to adapt to changing climate [1,5]. Gymnosperms xylem development, especially tracheid radial growth, have a significant influence on wood formation and adaptability under different environments [6]. No attempts have been made to explore the genetic factors underlying wood tracheid development variation. Uncovering the genetic basis of P. crassifolia wood tracheid traits is relevant for exploring the molecular mechanism of wood development in response to environmental changes
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