- QTL mapping for soybean (Glycine max L.) leaf chlorophyll-content traits in a. - Background: Different soybean (Glycine max L.) leaf chlorophyll-content traits are considered to be significantly linked to soybean yield. - In this study, 78 QTLs for soybean leaf chlorophyll-content traits were identified. - Conclusions: The detected QTLs and candidate genes may facilitate to gain a better understanding of the hereditary basis of soybean leaf chlorophyll-content traits and may be valuable to pave the way for the marker- assisted selection (MAS) breeding of the target traits.. - Keywords: Soybean, Leaf chlorophyll-content traits, QTL mapping. - Hence, a better understanding of the genetic basis of chlorophyll-content traits in soybean leaves may be valu- able for accelerating the soybean high-yield breeding.. - In general, the QTLs for soybean leaf chlorophyll-content traits are still lacking compared to other soybean traits. - In this study, we took the SPAD values as the indica- tors of the relative soybean leaf chlorophyll contents.. - For the assessments of these target soybean leaf chlorophyll-content traits, an advanced soybean RIL population (ZH RIL population) was adopted for the phenotypic data acquisitions. - In the current investigation, we consecutively collected the phenotypic data of the chlorophyll-content traits across different seasons and soybean reproductive growth stages. - Concomitantly, we ex- plored the relations between the QTLs identified in the present research and the published QTLs in the previous studies covering soybean leaf chlorophyll-content traits as well as soybean yield-related traits. - Finally, we pre- dicted six candidate genes for the target soybean leaf chlorophyll-content traits. - the current study may provide clues for future gene functional research on soybean leaf chlorophyll-content traits and may be useful for promoting MAS (mark- assisted selection) breeding of high-yield soybean varieties.. - To better map distinct QTLs for soybean leaf chlorophyll-content traits in the ZH RIL population, the phenotypic data and soybean leaf sam- ples were collected at 9 a. - Phenotypic frequency distributions of the target traits in the ZH RILs were depicted in Figs. - As is shown in the figures, the segregations of the chlorophyll-content traits fit normal or skew-normal dis- tribution models, with typical quantitative genetic char- acteristics. - Importantly, for each soybean leaf chlorophyll-content trait, the trans- gressive segregations widely presented in the RILs sug- gesting that the positive or negative alleles existed in the parent soybeans. - Correlation analyses of the phenotypic data in RILs turned out that most chlorophyll-content traits were strongly correlated under the specific testing method (SPAD testing or spectrophotometer assessing of leaf extracts) and showed statistically significant (P <. - stage in the summer of 2017). - Mapping for the chlorophyll-content QTLs by using a genotyped high-density bin marker linkage map. - In contrast, 19 extracting chlorophyll content QTLs were identified and distributed on the 12 soybean. - 1 Frequency distributions for leaf SPAD-related traits in the ZH RILs. - Explorations of important bin markers and QTL hotspots for soybean leaf chlorophyll-content traits. - As is shown in Table S6 (Additional file 1), five bin markers on four soybean chromosomes and 15) were determined to be important and each of them identified QTLs for at least two distinct chlorophyll- content traits. - In conclusion, the important bin markers may be valuable to detect the different chlorophyll-content QTLs throughout the environments.. - These QTL hotspots contained at least two QTLs and were named after ‘CT’, which represented their regulations on different chlorophyll-content traits (Table 2). - 2 Frequency distributions for leaf extracting chlorophyll content traits in the ZH RILs. - a the frequency distributions for leaf extracting chlorophyll content traits at soybean R1 growth stage in the summer of 2017 at Zengcheng. - b the frequency distributions for leaf extracting chlorophyll content traits at soybean R4 growth stage in the summer of 2017 at Zengcheng. - QTL hotspots, which included different SPAD and extracting chlorophyll content QTLs. - And qCT7Z con- tained two extracting chlorophyll content QTLs and three SPAD QTLs and located in a block from to bp on chromosome 07. - Moreover, qCT15Z-1 consisted of two SPAD QTLs and one extracting chlorophyll content QTL. - Notably, qCT15Z-1 Table 1 Leaf chlorophyll-content traits in the ZH RIL population across different environments. - 3 Soybean high-density genetic map of the ZH RIL population. - The 16 chlorophyll-content traits QTL hotspots were depicted in bold and the 13 major QTLs were marked by asterisks in bold. - Table 2 16 QTL hotspots associated with leaf chlorophyll-content traits detected in the ZH RIL population. - a The name of the QTL hotspot is a composite of multiple chlorophyll-content traits (CT). - b The name of the QTL is a composite of the chlorophyll-content traits: TSP: Top leaves SPAD value, MSP: Mid leaves SPAD value, BSP: Bottom leaves SPAD value, ASP: Average SPAD value, Chl_A: Chlorophyll a content, Chl_B: Chlorophyll b content, Chl_A/B: Chlorophyll a/b ratio. - The 16 chlorophyll- content traits QTL hotspots were marked in bold on the high-density genetic map. - In this study, we ana- lyzed the relations between the identified soybean leaf chlorophyll content traits QTLs and the published SPAD QTLs (Additional file 1: Table S8). - And most identified QTLs in the current research were novel ones for soybean leaf content traits.. - Based on the identical mapping popula- tion and the genetic map, we further explored the correlations between the chlorophyll-content QTLs in this study and the yield-related traits QTLs reported by Liu et al. - As a result, 19 identified chlorophyll-content QTLs spanned on eight chromosomes and 19) were found to be associated with the 25 published yield-related QTLs (Fig. - Concomitantly, both the detected chlorophyll-content traits major QTLs and the published yield-related traits major QTLs were highlighted with the purple diamond tags on the genetic linkage map. - Besides, different recorded yield-related traits QTLs on SoyBase were also found in the genetic regions of the five important QTL hotspots in this study (Additional file 1: Table S9). - In conclusion, the correlated chlorophyll- content and yield-related QTLs in the present and previ- ous studies, especially the major QTLs, may be valuable to pave the way for soybean high-yielding breeding.. - To gain an in-depth understanding of which genes may relate to soybean leaf chlorophyll-content traits, we re- trieved the gene calls in the genetic blocks of the 13 major QTLs and the five important QTL hotspots. - Totally 515 and 410 annotated genes were found in the corresponding hereditary intervals of the major QTLs and important QTL hotspots, respectively (Additional file 1: Table S10 and Table S11). - Based on the GO enrichment analyses, the gene annota- tions on SoyBase (Additional file 1: Table S14) and the gene expression levels on SoyBase and Phytozome (https://phy- tozome.jgi.doe.gov/pz/portal.html), we predicted six candi- date genes for soybean leaf chlorophyll-content traits.. - The genomic positions of the candidate genes were step- wise displayed from the anchored bin markers on soybean chromosomes to the candidate genes in the bin markers.. - Variations in soybean leaf chlorophyll-content traits Chlorophylls are the major photosynthetic pigments act- ing as the main absorbers of harvesting light in plants. - The chlorophyll-content QTLs and the published yield-related QTLs were colored in red and blue, respectively [24]. - Both the major QTLs for chlorophyll-content traits and yield traits were emphasized and marked with the purple diamonds. - a, in the summer of 2012. - b, in the summer of 2015. - Soybean chlorophyll-content traits are complex quantitative traits involving in the dual-effects of heredi- tary and environmental factors [48, 49]. - As is shown in Table 1, the phenotypic data of chlorophyll-content traits fluctuated with the soybean growth stages. - Moreover, according to the cor- relation analyses in Table S1 (Additional file 1), most chlorophyll-content traits were highly correlated under specific chlorophyll assessing methods. - For the mechanisms, the SPAD testing method is a non- destructive way that measures light transmittance of the leaf in the red and infrared wavelengths at 650 and 940 nm to assess the relative total chlorophyll content in leaves [5]. - The bin markers were corresponding to different chlorophyll-content traits QTLs in this study. - In all, var- iations of the soybean leaf chlorophyll-content traits support the reported characteristics of quantitative traits [29–31].. - This study aimed to explore QTLs for soybean leaf chlorophyll-content traits.. - Some chlorophyll- content traits QTLs were identified by the bin markers that spanned relatively large genetic intervals (Additional file 1: Table S6). - Notably, the parental soybeans broadly exhibited differences in the chlorophyll-content traits (Table 1, Figs. - Previous studies demonstrated that the significant positive correlations between seed yield and leaf chlorophyll content were usually found in soy- bean reproductive stages [7]. - In conclusion, the detected QTLs in the current study expanded the QTLs for soy- bean leaf chlorophyll-content traits and may be benefi- cial to soybean MAS breeding for associated soybean leaf chlorophyll-content traits.. - Correlations between the identified chlorophyll-content traits QTLs and reported diverse traits QTLs. - Hence, our findings may facilitate to enrich the genetic information for soybean leaf chlorophyll-content traits QTLs.. - In this study, we carried out comprehensive comparisons between the identified chlorophyll-content traits QTLs and the published yield-related QTLs. - Besides, we found some recorded yield-related QTLs on SoyBase located in genetic intervals of the five important QTL hotspots for chlorophyll-content traits (Additional file 1: Table S9). - This study focused on the QTL map- ping of distinct soybean leaf chlorophyll-content traits and we also investigated the relations between the iden- tified QTLs for soybean leaf chlorophyll-content traits in the current study and the early reported QTLs for soy- bean yield-related traits. - However, future phenotyping and correlation analyses between the soybean leaf chlorophyll-content traits and relevant yield traits still need to be performed to further explore the underlying relations between leaf chlorophyll content and soybean yield.. - Six candidate genes for the chlorophyll-content traits The leaf chlorophyll contents were determined by the dynamically biosynthesis and metabolism of chlorophylls in plant leaves [58]. - Based on the gene annotations and expression levels of the identified genes, we predicted six candidate genes for chlorophyll-content traits in the hereditary intervals of the major QTLs and the QTL hotspots. - Notably, the chlorophyll content was reported to be related to the nitrogen supply in soybean leaves [64]. - To sum up, the putative candidate genes may be useful for promoting the research on the hereditary basis of chlorophyll- content traits in soybean leaves.. - In this study, we mapped QTLs of seven soybean leaf chlorophyll-content traits by utilizing a genotyped ad- vanced recombinant inbred line population (ZH, Zhonghuang 24 × Huaxia 3) and its well-constructed high-density genetic map. - A total of 78 target traits QTLs were identified and most detected QTLs were novel QTLs for soybean leaf chlorophyll-content traits.. - Besides, six putative candidate genes were predicted from the hereditary regions of the major QTLs and important QTL hotspots. - Measurements of chlorophyll-content traits and data analyses. - Due to the diverse growth rates of the RILs, the phenotypic data for the chlorophyll-content traits were collected across dif- ferent periods. - Assessing chlorophyll content in leaf with the SPAD chlorophyll meter is a quick, cheap and effective approach to gain the phenotypic data for soybean leaf chlorophyll- contents. - Frequency distribution graphs of chlorophyll-content traits (TSP, MSP, BSP, ASP, Chl_A, Chl_B and Chl_A/B) were depicted by Graphpad Prism 7.0 (http://www.graphpad.com. - Comprehensively considering the gene annota- tions and gene tissue expression levels, the candidate genes for chlorophyll-content traits were predicted.. - Additional file 1: Table S1: The pairwise correlation coefficients between different chlorophyll-content traits in the ZH RILs across environ- ments. - Table S2: Correlation coefficients between different environments for leaf chlorophyll-content traits in the ZH RILs. - Table S3: Number of SNPs in the bin markers. - Table S6: The 78 QTLs and 70 loci for leaf chlorophyll-content traits in the ZH RIL population across different environments. - Information of Soybase published leaf chlorophyll-content traits QTLs;. - Table S8: Comparisons of the detected chlorophyll-content QTLs with. - Table S9: Five important chlorophyll- content traits QTL hotspots are associated with several reported yield- related QTLs on SoyBase. - Table S10: Genes in the hereditary intervals of the 13 major chlorophyll-content trait QTLs. - Table S11: Genes in the her- editary intervals of the five important QTL hotspots. - Table S15: Details of field trails, meteorological conditions and soybean growth stages used to determine the soybean leaf chlorophyll-content traits.. - S1: Distribution of the SNP loci throughout 20 soybean chromosomes in the ZH RIL population.. - S3: Visualization of the filtered GO enrichment terms. - CT: Chlorophyll-content traits. - LOD: Logarithms of the odds. - QTL analysis for dynamic expression of chlorophyll content in soybean (Glycine max L. - Comparison between QTLs for chlorophyll content and genes controlling chlorophyll biosynthesis and degradation in Japonica rice
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