- Assessment of heterosis based on parental genetic distance estimated with SSR and SNP markers in upland cotton ( Gossypium hirsutum L.). - Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid breeding.. - The objectives of this study were to estimate the GD between parents using both simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) markers and to investigate the efficiency of the prediction of hybrid performance based on GD. - The correlation of the GD. - assessed by both SSR and SNP markers was significantly positive. - The cluster analysis based on GD results estimated using SNP showed that all the female parents divided into five groups and the F 1 performance between these five groups showed significant differences in four traits, including lint percentage, micronaire, fiber strength, and fiber elongation ratio. - The correlation between GD and F 1 performance, MPH and BPH were significant for lint percentage and micronaire.. - Conclusions: Our results suggested that GD between parents could be helpful in heterosis prediction for certain traits. - Cotton is the most important natural fiber crop in the world and one of the cultivated allotetraploid Up- land cotton (Gossypium hirsutum L.) fulfills about 95% of the output of global cotton production [1].. - With the aim of saving resources, the genetic distance (GD) inferred from molecular markers has been sug- gested as a promising tool for hybrid performance pre- diction and recognition of heterotic groups [8–10].. - But these stud- ies were based on a rather small set of parental lines and the marker density was very low. - We used both SSR and SNP markers to estimate the GD between parents.. - We further analyzed the relationship between GD and heterosis, and assessed the feasibility of the use of SSR and SNP based genetic distances in predicting the hybrid performance and heterosis.. - Genetic distance and clustering analysis for the population. - In this study, both SSR and SNP markers were used to investigate the genetic distance (GD) between parents. - The GD between the parents calculated based on SSR markers showed that the GD between four male parents (Zhong7886, A971, 4133, and SGK9708) and 282 female parents varied from 0.139 to 0.387, with an average of 0.279 (Table 1, Table S1). - The GD between parents based on SNP markers showed that the GD varied from 0.137 to 0.375, with an average of 0.242 (Table 1, Table S1).. - The mean value of GD assessed by SNP markers in each F 1 populations was A >. - The correlation of the GD assessed by SSR and SNP markers was significantly positive (0.264 ≤ r ≤ 0.375, P <. - Furthermore, 1128 F 1 hybrids clustered into five groups based on GD assessed through SNP markers and named as group I, II, III, IV and V, having and 280 F 1 , re- spectively (Fig. - Table 1 Summary of genetic distance estimated between parents using both SSR and SNP markers. - Moreover, because the number of the SNP marker was significantly larger than SSR marker, so we decided to use the clustering results by SNP to do the further analysis.. - Furthermore, we evalu- ated the F 1 performance of the Elite×Elite, Exotic×Elite, and Historic×Elite hybrids and made comparisons with parent performances, and the result showed that all the F 1 hybrid performance were significantly higher than parents in all the nine traits except of fiber strength (Fig. - 1 Clustering of 1128 F 1 s into five groups using genetic distance based on SNP markers. - From the above clustering result by SNP, we con- cluded that all 1128 hybrids could be divided into five groups according to the GD, therefore we compared the F 1 hybrid performance of the each group and par- ents (Fig. - The mean values of MPH of the ten traits ranged from 0.09 to 14.18%, with an average of 4.36%, and the mean values of BPH ranged from − 4.85 to 3.30%, with an average of − 0.86%. - Generally, the mean BPH values were lower than the MPH values for all traits, and ap- proximately 80.9 and 41.6% of the crosses had positive MPH and BPH, respectively (Fig. - 1.81 to 2.76%) and BPH. - The correlation analysis between the performance of parents and the hybrid performance was studied to investigate the effect of the parents on the perform- ance of the hybrids. - The result showed that the cor- relation between parents and F 1 s performance was significantly positive (ranged from 0.459 to 0.843) in the ten traits except BW and BN. - For BW, FE and SCI, the correlation between parent. - While, FL showed significant negative correlation between parents and MPH in population D. - For LP, significant negative correlation was observed between parents and MPH in population A and D, but showed significant positive cor- relation in population E. - For LP, the correl- ation between parents and BPH showed significant positive correlation in population C, D and E. - For FU, parents and BPH showed significant negative cor- relation in group A, C and D. - For FE, the correlation between parents and BPH showed significant positive correlation only in group A. - The correlation for FL between parents and BPH showed significant negative correlation only in group D. - Correlation between genetic distance and F 1 performance To understand the effect of genetic distance of the par- ents on the level of heterosis in hybrids, the correlations between genetic distance and the F 1 performance, MPH, and BPH were calculated.. - Based on the correlation between the GD of SSR markers and F 1 performance, the GD SSR was negatively correlated with BW, LP, BN, FL, MIC, and FU in at least one F 1 population, but not significantly correlated with PH, FE and SCI (Table 2). - Based on the correlation between the GD of SNP markers and F 1 s performance, GD SNP was negatively correlated with LP, BN, FL, MIC and FE in at least one F 1 population but not significantly correlated with other traits like PH, BW and FS (Table 2). - Overall, most of the traits were negatively correlated with GD SSR and GD SNP , and only two traits (FS and SCI) were positively correlated with GD SSR and GD SNP in. - Relationship between genetic distance and MPH. - The correlation between GD of SSR markers and MPH showed that GD SSR was negatively correlated with FL, FS, MIC, FU, and SCI in population E, but positively correlated with MPH for PH and BW in population E and D, respectively (Table 3). - The correlation results be- tween GD of SNP markers and MPH showed that the GD SNP was positively correlated with the MPH of PH, BN, FS and FU in only one population and positively correlated with BW and SCI in two populations (Table 3). - For the MPH of LP, the correlation was posi- tive in the D population but negative in population E.. - In summary, the overall analysis results of the correl- ation between GD SSR and GD SNP in the four populations was inconsistent, and the correlation of group E was stronger than that of other groups.. - Relationship between genetic distance and BPH. - The correlation results between GD of SSR markers and BPH showed that the GD SSR was negatively correlated with the BPH of LP, FL, FS, MIC, FU, and SCI but posi- tively correlated with the BPH of PH (Table 4). - From the correlation results between GD of SNP markers and BPH, we observed that the GD SNP was negatively corre- lated with the BPH of LP, BN, FL, MIC, and FE, and positively correlated with the BPH of PH and BW (Table 4).. - In summary, the overall analysis results of the correl- ation between GD SSR , GD SNP and the BPH of ten traits were consistent. - Genetic distance between parents assessed by SSR and SNP markers. - Earlier at the end of the twentieth century, some studies have used RFLP and SSR markers to study the relationship between GD and heterosis, and proposed that the relationship between GD and heter- osis could be predicted by genetic differences [17].. - Subsequently, a number of studies used RAPD [18], AFLP [19, 20], SSR EST-SSR [24, 25], insertion-deletion (InDel) [11] and SNP markers to study the relationship between GD and heterosis. - Previous studies used different molecular marker types and those results were also different, but the GD was not compared. - SSR markers amplify products of different lengths according to the differ- ent number of tandem repeats in the core sequences of different materials to obtain the different genotypes of the population. - In this study, both SSR and SNP markers were used to study the GD between parents. - 0.05) and we found that the SNP marker was more Table 2 Correlation coefficients (r) of genetic distance with F 1 s performance of yield and fiber quality-related traits based on SSR and SNP marker.. - GD SSR : genetic distance calculated based on SSR marker. - GD SNP : genetic distance calculated based on SNP marker. - Table 3 Correlation coefficients (r) of genetic distance with mid-parent heterosis (MPH) of yield and fiber quality-related traits based on SSR and SNP marker.. - BN FL FS MIC FU FE SCI GD SSR : genetic distance calculated based on SSR marker. - accurate and efficient than SSR marker to study the relationship between GD and heterosis.. - Plant heterosis prediction based on genetic distance In recent years, methods have been sought to allow ini- tial selection of parents intended for heterosis crossing.. - In this study, under the condition of grouping according to different male parents, the GD of the two molecular markers were significantly nega- tively correlated with F 1 s performance and BPH of LP and MIC. - The correlation between GD and MPH of each trait was weak. - The correlation between GD SNP. - and F 1 s performance, MPH and BPH was stronger than that of GD SSR . - In addition, according to the clustering result by GD based on SNP, we found that all the F 1 s could be divided into five groups, and its average values of GD was and 0.261 for Group I, III, IV, V and II, respectively (Fig. - All these results indicated that genetic distance between parents can be a valuable indicator for heterosis predication, es- pecially for lint percentage micronaire, fiber length, and fiber elongation ratio and F 1 crosses clustered in Group II had more commercial values in hybrid cotton breeding.. - In maize, the GD between parental components, as determined by the SNP and SilicoDArT markers was significantly correlated with the heterosis effect observed in the majority of the yield structure features, as well as the yield itself [12]. - reported a significant cor- relation between GD and MPH of 1000-grain weight in wheat [13]. - found a positive correlation for the genetic dis- tance of the inbred lines from the common Brassica napus parent with MPH for seed yield (r = 0.31) and hybrid yield (r . - observed weak associations between the GD based on SNP and MPH or BPH of spikelet number, harvested spikes and yield in Table 4 Correlation coefficients (r) of genetic distance with best-parent heterosis (BPH) of yield and fiber quality-related traits based on SSR and SNP marker.. - found GD based on SSR markers poorly correlated with F 1 performance, MPH and SCA in wheat [30]. - found that the GD was not corre- lated with heterosis of grain yield in pearl millet [21]. - In a previ- ous study of maize lethal necrosis, a very low and negative correlation was observed between parental lines marker- based genetic distance and heterosis [31].. - Previous studies showed that the efficiency of predicting heterosis by GD esti- mates was improved by selecting markers tightly linked to the QTL affecting heterosis of the target trait [34].. - In this study, we used both SSR and SNP markers to es- timate the GD between parents and to investigate the ef- ficiency of the prediction of hybrid performance based on GD. - Our study found that all the female parents could be divided into five groups based on GD SNP clus- ter result and the F 1 performance between these five groups showed significant differences in LP, MIC, FS, and FE. - Furthermore, the correlation between GD and F 1 performance, MPH and BPH were significant negative for lint percentage and micronaire. - All the seeds were stored in the National Germplasm Mid-term Bank of the Institute of Cotton Research (ICR), the Chinese Academy of Agricultural Sciences (CAAS). - The probability of the fragments mapped to the reference genome was the coverage on the genome was 0.07–7%, and the average sequencing depth was 1.48. - Evaluation of genetic distance and correlation analysis The genetic distance (GD) of SSR markers between par- ents was determined according to Nei’s et al. - The GD of SNP markers between parents were calculated by TASSEL 5.0 based on the identity-by- state (IBS) genetic distance as GD SNP = 1-IBS [41]. - The average performance of MPH and BPH of ten yield and fiber quality related traits of 1128 F 1 s were analyzed by Graphpad prism 7.0. - The packages ggplot2 and GGally in R software were used to analyze the correlation be- tween GD of SSR and SNP marker and F 1 s performance, MPH, and BPH. - Additional file 1 Table S1 Genetic distance matrix between parents assessed with SSR and SNP markers.. - S2 Clustering of 1128 F 1 s into three groups using genetic distance based on SSR markers. - A, Clustering result by genetic distance based on SSR markers. - S3 Boxplots showing the distribution of genetic distance for the Elite×Elite, Exotic×Elite, and Historic×Elite hybrids.. - GD: Genetic distance. - We are grateful to the National Germplasm Mid-term Bank of the Institute of Cotton Research (ICR), the Chinese Academy of Agricultural Sciences (CAAS) for providing all the cotton germplasms.. - Assessment of heterosis based on genetic distance estimated using SNP in common wheat. - Relationship between SSR-based genetic distance and cotton F 2 hybrid performance for lint yield and fiber properties. - A diallel analysis of heterosis in elite hybrid rice based on RFLPs and microsatellites. - Relationship of parental genetic distance with heterosis and specific combining ability in sesame (Sesamum indicum L.) based on phenotypic and molecular marker analysis.. - Potential of the C genome of the different variants of Brassica oleracea for heterosis in spring B napus canola. - Combining ability, heterosis, genetic distance and their intercorrelations for waterlogging tolerance traits in chrysanthemum. - for yield and vigor traits from 34 hybrid families in Costa Rica based on the genetic basis of the parental population. - Relationship of genetic distance and hybrid performance in hybrids derived from a new photoperiod-thermo sensitive male sterile wheat line 337S
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