Association Analysis Of 43 Traits With SNP Markers In 150 Durum Wheat Accessions

Both tetraprum durum wheat?Triticum turgidum L.durum?Desf.?,AABB,2n=4x=28?,and common wheat?Triticum aestivum L,AABBDD,2n=6x=42?belong to the genus Triticum?Triticum spp.?of Poaceae.The planting area of durum wheat accounts for about 10%of the total planting area of common wheat in the world.Durum wheat has two common genomes with common wheat,so it is an important basic material for secondary gene resources and wheat variety improvement.Knowledge of inheritance of main traits of durum wheat is only efficiency improveing durum wheat,but also promote for breeding of common wheat.The seedling traits have a basic effect on the formation and yield factors of wheat in the middle and late stages.The canopy of leaf?flag leaf,second leaf and third leaf?in wheat plays an important role in the whole life cycle of wheat.It is not only the main organ of photosynthesis in wheat,but also produces more than 80%of primary nutrients for wheat grains through photosynthesis after heading.Therefore,the study of canopy leaf related traits in durum wheat can help to better understand the potential genetic basis of functional leaves,and it is important to select high-efficiency ideal plant type and increase grain yield for durum wheat and common wheat.The 1000-grain weight of wheat is a relatively complex trait,which is largely controlled by some grain traits?grain size,grain morphology,etc.?.It is of great significance for further excavating excellent alleles and promoting the genetic improvement of target traits such as wheat yield.In this study,seedling traits?seed height,leaf,root and biomass related traits?of hydroponic culture and functional leaf traits?leaf length,leaf width,leaf area and chlorophyll content?at heading stage and grain traits?grain morphology and 1000-grain weight?for 150 durum wheat materials from 41countries and regions in the world using 1366 single nucleotide polymorphism?SNP?markers covering the whole genome of durum wheat were associated mapping.The main results were summarized as follows:1.Analysis of seedling traits in durum wheat:The 21 traits of durum wheat seedlings were abundant in phenotypic variation,and the generalized heritability of 17 traits was greater than 75%,indicating that the heritability of seedling traits was higher.Among 210correlation coefficients,137 were significant or extremely significant.For example,the dry weight of the aboveground part was significantly positively correlated with the total dry weight,plant height was significantly negatively correlated with root length.A total of90 SNP markers significantly associated with 21 traits at seedling stage were detected.Among them,88 SNP markers significantly associated with 18 seedling traits at four stages?13d,20d,27d and 34d?and 35 SNP markers significantly associated with 3seedling biomass traits?total biomass,root dry weight and shoot dry weight?were detected.These markers were distributed on 14 chromosomes of durum wheat.It is mainly concentrated on chromosomes 1A,1B,4A,5B,6B and 7A,and the R² value ranges from 7.5%to 20.59%.Ten SNP markers were repeatedly detected in two or more of the four periods of the seedling stage,of which four SNP markers?BG314205_1B33,BE443538_5A1436,BE590521_6BN331,and BG313722_3A281?were associated with two seedling traits.2.Analysis of canopy leaf traits in durum wheat:There are abundant phenotypic variations among the 14 canopy leaf traits measured in the heading stage of durum wheat.The Shapiro-Wilk method was used to test the three-year normal distribution of data.The results showed that most of the traits conform to the normal distribution.Among the 91correlation coefficients that may exist,63 extremely significant or significant correlations were found.There was a significant positive correlation between the upper second leaf area and total area of the top three leaves.The upper third leaf length was significantly negatively correlated with average chlorophyll content of top three leaves.A total of 83significantly associated SNP markers were detected for 14 leaf traits in three years,of which 9 were detected in 2015,55 were detected in 2016,and 41 were detected in 2017.These markers are distributed on all other chromosomes except for 3B in durum wheat,but mainly on chromosomes 2A,3A,6B,7A and 7B.A total of 31 multi-effect SNP markers were found to be associated with leaf morphological traits?leaf length,leaf width,leaf area?for three years,including 28 SNP markers significantly associated with leaf length,30 SNP markers significantly associated with functional leaf width and 29 SNP markers significantly associated with functional leaf area.These SNP markers detected in3 years were mainly distributed on the 4B,5B and 6B chromosomes of durum wheat and the R² rang was 7.37%to 46.39%.There are 3 multi-effect candidate genes?BE585760_2AY481,R²?15.04%;CD452967_5BY229,R²?15.95%and BE637485_5BY219,R²?45.52%?associated with all functional leaf traits.Meanwhile,59 SNP markers significantly associated with chlorophyll content of functional leaves?the flag leaf chlorophyll content,FLCC,the upper second leaf chlorophyll content,SLCC and the upper third leaf chlorophyll content,TLCC?were detected in three years.38 SNP markers were significantly associated with FLCC,7 SNP markers were significantly associated with SLCC,and 18 SNP markers were significantly associated with TLCC.These SNP markers were mainly distributed on chromosomes 1A,2A,4A,5B and 7A of durum wheat,the R² rang was 8.81%to 38.01%.In 2016 and 2017,20 SNP markers were repeatedly detected,including 4 multi-effect candidate genes?BE490384_2AY544,R²?14.97%;BE585760_2AY481,R²?34.89%;CD452967_5BY229,R²?37.69%and BG274019_2BN260,R²?16.45%?significantly associated with both FLCC and SLCC.3.Analysis of grain-related traits in durum wheat:Eight grain traits?grain area,grain perimeter,grain width,grain length,grain aspect ratio,grain roundness,grain diameter and 1000-grain weight?of durum wheat mature seeds were measured.It was found that the difference between the grain area and the 1000-grain weight was relatively large,and the coefficient of variation?CV?was relatively high.The difference between the other 6traits was small,and the coefficient of variation was small?<10%?.Shapiro-Wilk method was used to test the normal distribution of five-year grain morphological data and three-year 1000-grain weight data.Except for grain length and grain length/width ratio,other traits basically conformed to the normal distribution.The correlation analysis of 7grain morphological traits showed that 26 correlation coefficients were significantly or extremely significantly correlated.The roundness of grains was negatively correlated with other grain morphological traits?except grain width?,while the other 6 grain traits were positively correlated.In the five years,a total of 61 significantly associated SNP markers were detected in 7 grain morphological traits?15 were detected in 2014,20 were detected in 2015,25 were detected in 2016,9 were detected in 2017,and 14 were detected in2018?.The number of the grain length/width detected was the highest?32?in the five years,followed by grain roundness?19?and grain width?18?.Among them,10 SNP markers?BE352626_4AY110,BE404377_4BY333,BE500291_5A37,BF474023_3AY425,BF474862_5A762,BJ291318_5BY242,BM140538_2B133,BQ168780_5B995,CD452967_5BY229and CD453605_6B427?are repeatedly detected for at least two years.A total of 10significantly associated SNP markers associated with 1000-grain weight were detected in three years.All SNP markers associated with 8 grain traits were distributed on all chromosomes of durum wheat,but mainly distributed on chromosomes 2A,4A,5A,6A,6B and 7A.The range of R² was 4.67%⁴4.72%.The coefficients of variation of 43 traits measured in 150 durum wheat materials ranged from 2.4%to 22.8%,and the generalized heritability?H²?was higher?50%⁹5%?.This indicated that there were abundant genetic differences among the tested durum wheat materials,which were an important genetic resource for wheat genetic improvement.The182 SNP markers significantly associated with the 43 traits of durum wheat,including seedling traits,leaf traits,and grain traits,clearly identified the distribution characteristics of these SNP markers on the durum wheat chromosomes.It has a positive effect on understanding the gene expression characteristics of durum wheat at seedling stage,heading stage and maturity stage,and has important significance for the genetic improvement of durum wheat and common wheat.