Construction Of DNA Fingerprint And Genetic Diversity Of Upland Cotton Varieties In Xinjiang

?Object?Cotton(Gossypium hirsutum L.)is an important fiber crop.Xinjiang is the largest commercial cotton production and cotton seed base in China.The quality of cotton seeds is the fundamental to ensure the healthy development of cotton industry.However,the current situation of the cotton seed market is numerous,chaotic,some varieties with the phenomenon of “deck”,which seriously affects the quality of cotton and the income of cotton farmers in Xinjiang,the healthy development of the cotton industry also jeopardized.In order to effectively improve the quality of cotton,there are a lot of work to be done urgently,for instance,strengthening the quality sampling and supervision of all aspects in cotton seed production.The purpose of this study is to screen out polymorphic primers which are suitable for identifying upland cotton varieties in Xinjiang,to construct a DNA fingerprint and exclusive QR code for each of varieties,and to conduct genetic diversity analysis.It provides practical markers for molecular identification of upland cotton varieties in Xinjiang.Moreover,it can improve the quality of cotton seeds in Xinjiang and provide technical support for the quality inspection and supervision of cotton seeds.?Methods?In this study,SSR,STS and InDel markers were selected for core primer screening,with the characteristic and combined primer method,to complete the DNA fingerprint and exclusive QR code of upland cotton varieties in Xinjiang,and using NTSYS software to analyze genetic diversity.?Results?(1)(1)Using molecular markers with high polymorphism and good stability complete PCR amplification of 150 Xinluzao and Xinluzhong cotton varieties.52 pairs of primers detected 159 amplified band patterns,with amplified bands patterns ranged from 2 to 7 and an average of 3.06.A total of 307 amplified bands were obtained,and each marker detected 2~13 amplified bands,with a mean of 5.90;The number of polymorphic bands was 253,which range from 1 to 12 and an average of 4.87;the rate of polymorphic bands was 40.0%~100.0%.The polymorphism information content of 52 pairs primers was 0.183 2~0.767 8 with an average value of 0.479 7.Among the 150 Xinluzao and Xinluzhong cotton varieties,12 varieties had characteristic primers.With 20 pairs of primer combinations,150 Xinluzao and Xinluzhong cotton varieties could be distinguished completely.(2)NTSYS software was used to analyze genetic diversity of 150 Xinluzao and Xinluzhong cotton varieties,the results showed that 150 upland cotton varieties in Xinjiang could be categorized into 4 major groups at the genetic similarity coefficient of 0.705 6.The genetic similarity coefficient was 0.503 1~0.993 6 and an average of 0.706 4,showing the narrow genetic diversity in 150 upland cotton varieties.The genetic similarity coefficients of Xinluzao and Xinluzhong cotton varieties were 0.536 7~0.993 6 and 0.503 1~0.987 7,with the average of 0.716 3 and 0.719 2.The average genetic similarity coefficients of Xinluzao cotton varieties and Xinluzhong cotton varieties in different years were 0.693 8~0.743 4 with a little change.It is indicated that the problem of narrow genetic basis of land cotton in Xinjiang persists for a long time.Xinluzao cotton varieties showed a slight downward trend;Xinluzhong cotton varieties showed an upward trend in generally and recently showed a downward trend.(2)(1)Using the 52 pairs of core primers by screened,A total of 155 polymorphic band patterns were amplified in 27 color cotton varieties in Xinjiang,and each marker detected 2~7 polymorphic band patterns and an average of 2.98.The number of amplified bands was 348,which ranged from 2 to 17 and a mean of 6.69;the polymorphic bands was 263,with polymorphic bands ranged from 1 to 17 and an average of 5.06;the polymorphism rate was 40.0%~100.0%.The PIC value of 52 pairs of primers ranged from 0.137 1 to 0.776 4 and an average value of 0.454 3.Among the 27 colored cotton varieties in Xinjiang,12 varieties had characteristic molecular primers,and 7 combinated primers could distinguish the other 15 varieties;using 9 characteristic primers and combinated primers could distinguish 27 colored cotton varieties in Xinjiang completely.(2)Cluster analysis showed that the genetic similarity coefficients of 27 colored cotton varieties in Xinjiang were 0.412 2~0.955 9 and a mean of 0.650 6.It indicated that colored cotton varieties in Xinjiang was a relatively rich genetic basis,and green cotton had a higher genetic diversity than brown cotton.According to the genetic similarity matrix,27 colored cotton varieties in Xinjiang could be divided into 3 groups,and the UPGMA clustering analysis results are more consistent with the principal coordinates analysis.?Results?In this study,61 pairs of molecular markers with high polymorphism and strong discrimination ability were screened out,we were constructed DNA fingerprints of 177 upland cotton varieties in Xinjiang.The genetic basis of 150 upland cotton varieties in Xinjiang was narrow,and the genetic basis of 27 colored cotton varieties in Xinjiang was relatively rich.