Single Segment Substitution Lines Research Articles

Genetic dissection of QTLs and differentiation analysis of alleles for heading date genes in rice.

Heading date is an important agronomic trait in rice (Oryza sativa L.); it determines the geographical and seasonal adaptability of the crop. Single segment substitution lines (SSSLs) have become the preferred experimental materials in mapping functional genetic variations as the particular chromosome segments from donor genotypes can be evaluated for their impact on the phenotype in a recurrent recipient background. The phenotypic differences can be attributed to the control of quantitative trait loci (QTLs). Here, we evaluated a library consisting of 1,123 SSSLs in the same genetic background of an elite rice variety, Huajingxian74 (HJX74), and revealed four SSSLs, W05-1-11-2-7-6 (W05), W08-16-3-2 (W08), W12-28-58-03-19-1 (W12), and W22-9-5-2-4-9-3 (W22), which had a significantly different heading date compared to HJX74. To further genetically dissect the QTLs controlling heading date on chromosomes 3, 6, and 10, four SSSLs were used to develop 15 secondary SSSLs with the smaller substituted segments. The qHD-3 heading date QTL detected in W05 and W08 was delimited to an interval of 4.15 cM, whereas qHD-6-1 and qHD-6-2 heading date QTLs dissected from the substituted segments in W12 were mapped to the intervals of 2.25-cM and 2.55-cM, respectively. The qHD-10 QTL detected on the substituted segment in W22 was mapped to an interval of 6.85-cM. The nucleotide and amino acid sequence changes for those genes in the secondary SSSLs were also revealed. The allele variations of those genes might contribute to the heading date QTLs on chromosome 3 (DTH3, OsDof12, and EHD4), chromosome 6 (Hd3a, Hd17, and RFT1), and chromosome 10 (Ehd1 and Ehd2). These sequence variations in heading date genes would be useful resources for further studying the function of genes, and would be important for rice breeding. Overall, our results indicate that secondary SSSLs were powerful tools for genetic dissection of QTLs and identification of differentiation in the genes.

Effects of different Wx alleles on amylopectin molecular structure and enzymatic hydrolysis properties of rice starch

ABSTRACTAllelic variation at the Wx locus plays a vital role in regulating apparent amylose content (AAC) as well as other important starch properties in rice grain. However, the extent of Wx allelic variation affecting amylopectin fine structure and enzymatic hydrolysis properties of rice starch remains unknown. In this paper, a series of rice single-segment substitution lines with five different Wx alleles (wx, Wxt, Wxg1, Wxg2 and Wxg3) were used for comparative studies. The results showed that the five Wx alleles exhibited a wide variation in amylopectin molecular structure, hydrolysis and in vitro digestion properties of rice starch. Amylopectin chain length distribution as evaluated by fluorophore-assisted capillary electrophoresis was significantly different for the five Wx alleles, which might result in different functional properties. The hydrolysis degree of the five Wx genotype starches by α-amylase or amyloglucocidase was in the order wx > Wxt > Wxg1 > Wxg3 > Wxg2. The rapidly digestible starch (RDS) content of the tested rice starches followed the order wx = Wxg3 > Wxt = Wxg1 > Wxg2. The extent decrease of slowly digestible starch (SDS) content was wx = Wxt > Wxg1 > Wxg2 > Wxg3, while the trend in resistant starch (RS) content was Wxg2 > Wxg3 > Wxg1 > Wxt > wx. Correlation analysis indicated that AAC was significantly positively correlated with RS but significantly negatively correlated with SDS and hydrolysis. The RDS showed a significant positive correlation with amylopectin short chains (DP 6–12) but no significant correlations with other structural properties. The present results could provide important information for the application of rice starches with different Wx genotypes.

Development and trait evaluation of chromosome single-segment substitution lines of O. meridionalis in the background of O. sativa

O. meridionalis is a wild species belonging to AA genome in the Oryza genus, which has a lot of beneficial genes for improvement of cultivated rice. In the present study, 99 chromosome single-segment substitution lines (SSSLs) were developed carrying donor segments of O. meridionalis in the genetic background of an indica cultivar, Huajingxian 74 (HJX74). The total lengths of the 99 substituted segments in the SSSLs were 1580.16 cM, with an average length of 15.11 cM per substituted segment, covering 873.94 cM and 54.98% of O.meridionalis genome. Phenotypic investigations of the SSSLs showed that three SSSLs had red pericarp, awn and showed seed shattering, respectively, indicating that these genes of O. meridionalis responsible for these traits have been transferred to the SSSLs. And wide variations were observed in seven quantitative traits including heading date and yield-related traits in 82 SSSLs.At P ≤ 0.001, 77 SSSLs showed significant differences compared with HJX74 in at least one trait either in the fall of 2014 or spring of 2015, and a total of 28 stable QTLs were detected in 24 SSSLs in both seasons. These results suggest that the SSSLs library of O. meridionalis developed in this study offers a good germplasm platform for the identification and transformation of beneficial genes of O. meridionalis, and facilitates the conservation of gene resources of O. meridionalis in vivo for long periods.

Genetic dissection of top three leaf traits in rice using progenies from a japonica × indica cross.

The size of the top three leaves of rice plants is strongly associated with yield; thus, it is important to consider quantitative traits representing leaf size (e.g., length and width) when breeding novel rice varieties. It is challenging to measure such traits on a large scale in the field, and little is known about the genetic factors that determine the size of the top three leaves. In the present study, a population of recombinant inbred lines (RILs) and reciprocal single chromosomal segment substitution lines (SSSLs) derived from the progeny of a japonica Asominori × indica IR24 cross were grown under four diverse environmental conditions. Six morphological traits associated with leaf size were measured, namely length and flag leaf, length and flag, second and third leaves. In the RIL population, 49 QTLs were identified that clustered in 30 genomic region. Twenty-three of these QTLs were confirmed in the SSSL population. A comparison with previously reported genes/QTLs revealed eight novel genomic regions that contained uncharacterized ORFs associated with leaf size. The QTLs identified in this study can be used for marker-assisted breeding and for fine mapping of novel genetic elements controlling leaf size in rice.

Substitution mapping of QTLs controlling seed dormancy using single segment substitution lines derived from multiple cultivated rice donors in seven cropping seasons.

A permanent advanced population containing 388 SSSLs was used for genetic analysis of seed dormancy; 25 QTLs including eight stable, six major and five new were identified. Seed dormancy (SD) is not only a complex biological phenomenon, but also a key practical problem in agricultural production closely related with pre-harvest sprouting (PHS). However, the genetic mechanisms of SD remain elusive. Here, we report the genetic dissection of SD in rice using 388 single segment substitution lines (SSSLs) derived from 16 donor parents. Continuous variation and positive correlations in seed germination percentages were observed in seven seasons. Genetic analysis revealed the narrow sense heritability in different seasons varied from 31.4 to 82.2% with an average value of 56.8%. In addition, 49 SSSLs exhibited significant difference to recipient parent HJX74 on SD in at least two seasons, and 12 of them were stably identified with putative QTLs in all of their corresponding cropping seasons. Based on substitution mapping, a total of 25 dormancy QTLs were detected on 11 chromosomes except the chromosome 5 with an interval length of 1.1 to 31.3cM. The additive effects of these QTLs changed from -0.31 to -0.13, and the additive effect contributions ranged from 16.7 to 41.4%. Six QTLs, qSD3-2, qSD4-1, qSD7-1, qSD7-2, qSD7-3 and qSD11-2, showed large additive effect contributions (≥30%). Five QTLs, qSD3-3, qSD7-1, qSD7-4, qSD9-1 and qSD10-1, may represent novel ones. Furthermore, linkage and recombinant analysis delimited qSD7-1 to a locus 1.5cM away from marker Oi2 and a 355-kb fragment flanked by RM1134 and Ui159, respectively. Taken together, this work conducts a comprehensive genetic dissection of SD and will provide more selections for breeding elite PHS-resistant rice varieties.

Integrating Small RNA Sequencing with QTL Mapping for Identification of miRNAs and Their Target Genes Associated with Heat Tolerance at the Flowering Stage in Rice.

Although, microRNAs (miRNAs) have been reported to be associated with heat tolerance at the seedling stage in rice, their involvement in heat tolerance at the flowering stage is still unknown. In this study, small RNA profiling was conducted in a heat-tolerant variety Gan-Xiang-Nuo (GXN) and a heat-sensitive variety Hua-Jing-Xian-74 (HJX), respectively. Totally, 102 miRNAs were differentially expressed (DE) under heat stress. Compared to HJX, GXN had more DE miRNAs and its DE miRNAs changed earlier under heat stress. Plant Ontology (PO) analysis of the target genes revealed that many DE miRNAs were involved in flower development. As a parallel experiment, QTL mapping was also conducted and four QTLs for heat tolerance at the flowering stage were identified using chromosome single-segment substitution lines derived from GXN and HJX. Further, through integrating analysis of DE miRNAs with QTLs, we identified 8 target genes corresponding to 26 miRNAs within the four QTL regions. Some meaningful target genes such as LOC_Os12g42400, SGT1, and pectinesterase were within the QTL regions. The negative correlation between miR169r-5p and its target gene LOC_Os12g42400 was confirmed under heat stress, and overexpression of miR169r-5p enhanced heat tolerance at flowering stage in rice. Our results demonstrate that the integrated analysis of genome-wide miRNA profiling with QTL mapping can facilitate identification of miRNAs and their target genes associated with the target traits and the limited candidates identified in this study offer an important source for further functional analysis and molecular breeding for heat tolerance in rice.

Identification and pyramiding of QTLs for cold tolerance at the bud bursting and the seedling stages by use of single segment substitution lines in rice (Oryza sativa L.)

Cold stress is one of the main constraints in rice production, and damage from cold can occur at different developmental stages in rice. Understanding the genetic basis of cold tolerance is the key for breeding cold-tolerant variety. In this study, we used single segment substitution lines (SSSLs) derived from a cross between cold-tolerant japonica variety “Nan-yang-zhan” and a popular indica variety “Hua-jing-xian 74” to detect and pyramid QTLs for cold tolerance at the bud bursting and the seedling stages. Evaluation of cold tolerance of these SSSLs and their recurrent parent helped identify two cold-tolerant QTLs (qCTBB-5 and qCTBB-6) at the bud bursting stage and two cold-tolerant QTLs (qCTS-6 and qCTS-12) at the seedling stage. The SSSLs carrying these QTLs showed stronger cold tolerance than their recurrent parent HJX74 did in three independent experiments. The qCTBB-6 and qCTS-6 were mapped to the same chromosomal region. QTL pyramiding was performed by intercrossing of SSSLs carrying the respective QTLs for cold tolerance at the bud bursting stage and the seedling stage and marker-assisted selection (MAS). The selected pyramiding line SC1-1 with different cold-tolerant QTLs showed cumulative effects on cold tolerance. Our results suggest that different genes (QTLs) control cold tolerance at bud bursting and seedling stages, and pyramiding of stable expression QTLs for cold tolerance at different developmental stages through MAS is a good strategy to prevent cold damage in rice.

Detection of additive and additive×environment interaction effects of QTLs for yield‐component traits of rice using single‐segment substitution lines (SSSLs)

AbstractAdditive effects (A) and additive‐by‐environment interactions (A×E) for five rice yield components were analysed using 20 SSSLs under mixed linear model methodology. Thirty‐one QTLs were detected. Different yield components have different QTL‐by‐environment (Q×E) interaction patterns. No A×E interaction effects were detected for the four QTLs for panicle number (PN). Four QTLs detected for spikelets per panicle (SPP) had A×E interactions. Five of seven QTLs detected for grains per panicle (GPP), two of 10 QTLs detected for 1000‐grains weight (GWT) and three of six QTLs detected for seed set ratio (SSR) showed significant A×E interaction. Most of these QTLs were distributed in clusters across the genome. The complexity of linkage and pleiotropy of these QTLs plus environmental effect may result in the diversity of the yield phenotype in the SSSLs. Only S19 exhibited a significant increase in yield with a predicted gain by 281.58 kg ha−1. The results may be useful to design a better breeding strategy that takes advantage of QTL‐by‐environment interaction effects in each of the SSSLs.

Crystalline, thermal and swelling properties of starches from single-segment substitution lines with different Wx alleles in rice (Oryza sativa L.).

In rice, five common Wx alleles, wx, Wxt , Wxg1 , Wxg2 and Wxg3 , have been identified according to their apparent amylose content (AAC) phenotypes. Previous studies revealed that this Wx allelic variation may also affect other starch properties. However, so far, to what extent the five Wx alleles influence the crystalline structure, thermal and swelling properties of rice starch is still unclear. For this purpose, a set of single-segment substitution lines (SSSLs) harboring five different Wx alleles, varying widely in AAC, was used for comparative studies. The crystalline structure, thermal properties and swelling behavior of starches from the SSSLs varied widely depending on Wx genotype. Effects of different Wx alleles on relative crystallinity followed the order wx > Wxt > Wxg1 = Wxg2 > Wxg3 . The glutinous and Wxt genotype starches showed higher gelatinization temperatures and enthalpy compared with other Wx genotypes. The order for swelling power was wx > Wxt > Wxg1 > Wxg2 > Wxg3 , while the order for degree of solubility was Wxg3 > Wxg1 > Wxg2 > Wxt = wx. Correlation analysis indicated that AAC was significantly and negatively correlated with relative crystallinity (r = -0.996, P < 0.01) and swelling power (r = -0.982, P < 0.01). The present results provide new knowledge about the influence of different Wx alleles on the structural and physicochemical properties of rice starch. © 2016 Society of Chemical Industry.

Genetic analysis of heterosis for maize grain yield and its components in a set of SSSL testcross populations

The present study aimed to dissect the genetic basis of heterosis for grain yield and its components in maize (Zea mays L.). Quantitative trait loci (QTL) and heterotic loci (HL) were analyzed using a set of 203 single segment substitution lines (SSSLs) and its testcross population in three environments. Forty-one QTL were identified as responsible for grain yield, ear length, ear diameter, row number, kernel number per row, and 100-kernel weight in the SSSLs population, and 17 QTL were conserved across the three environments. In the heterosis analysis, 36 HL were identified for grain yield and five yield-related traits in the test population in the three environments. Among the HL, only six (16.7 %) for ear length, kernel number per row, 100-kernel weight, and grain yield were consistent with the results of QTL mapping. In addition, 16.7 % of the heterotic loci showed a dominant effect and 83.3 % showed an over-dominant effect. The results implied that dominance and over-dominance were two important components of heterosis in maize grain yield and yield-related traits in the present testcross population.

Development of a platform for breeding by design of CMS restorer lines based on an SSSL library in rice (Oryza sativa L.).

Exploitation of the heterosis of hybrid rice has shown great success in the improvement of rice yields. However, few genotypes exhibit strong restoration ability as effective restorers of cytoplasmic male sterility (CMS) in the development of hybrid rice. In this study, we developed a platform for the breeding by design of CMS restorer lines based on a library of chromosomal single segment substitution lines (SSSLs) in the Huajingxian74 (HJX74) genetic background. The target genes for breeding by design, Rf34 and Rf44, which are associated with a strong restoration ability, and gs3, gw8, Wxg1 and Alk, which are associated with good grain quality, were selected from the HJX74 SSSL library. Through pyramiding of the target genes, a restorer line, H121R, was developed. The H121R line was then improved regarding blast resistance by pyramiding of the qBLAST11 gene. Hence, a new restorer line with blast resistance, H131R, was developed. The platform involving the Rf34 and Rf44 restorer genes would be used for the continuous improvement of restorer lines through breeding by design in rice.

Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes.

A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

Transcriptomic analysis of maize kernel row number-associated miRNAs between a single segment substitution line and its receptor parent

To detect microRNAs (miRNAs) involved in determining kernel row number in maize, next generation deep sequencing was performed on an elite inbred line Zong3 (row number 14–16) of maize in China and a single segment substitution line (SSSL) SSL-10 (row number 8–10) derived from the same genetic background. In SSL-10, the single segment is inserted in chromosome 1 between molecular marker bnlg1953 and bnlg1811. Twenty-eight miRNAs belonging to 11 conserved miRNA families in maize showed expression differences >2-fold in the two lines, among which 14 members from four miRNA families were up-regulated and 14 members from 7 miRNA families were repressed in SSL-10. A genome wide degradome was sequenced to validate the miRNA target genes in solid experiment. In addition, novel miRNAs associated with ear development were predicted using a series of strict criteria, and 29 miRNAs representing eight families were predicted as novel miRNAs. Among the novel miRNAs, only one showed an expression difference >2-fold. The conserved and novel miRNAs with >2-fold expression differences were treated as candidate miRNAs involved in maize kernel row number determination. MiRNA-dependent gene expression regulation and physiological and morphological effects on ear development may explain why the SSSL changed kernel row number compared with its recurrent parent. Based on the interaction of miRNAs and their target genes, a possible miRNA-dependent pathway leading to the given DNA fragment inducing a change in kernel row number was proposed.

Bigenic epistasis between QTLs for heading date in rice analyzed using single segment substitution lines

Accumulating evidences suggested that epistasis, interactions between genes, is an important component of the genetic determination of quantitative traits. In present study, four F2 populations derived from pair wise crosses between 5 single segment substitution lines in the HJX74 background, harboring single QTL for heading date including Hd3a, RFT1, OsFTL13, OsMADS50IR64 and OsMADS50Lemont were used to characterize the epistasis between QTLs and QTL-by-environment interaction (QEI). Epistasis was found to be present between Hd3a and OsMADS50IR64, Hd3a and OsMADS50Lemont, and RFT1 and OsMADS50IR64. The interaction between Hd3a and OsFTL13 was not detected by single environment analysis but detected by across-environment combined analysis. Genetic analysis using a bigenic model showed that the additive and dominant effects were more important than the overall epistatic effects for all pairs of QTLs. The additive-by-additive and additive-by-dominant effects were more important than the dominant-by-dominant effect. QEIs were significant for Hd3a, RFT1, OsMADS50IR64 and OsMADS50Lemont but not for OsFTL13. The additive-by-environment and dominant-by-environment interaction effects were significant while the epistasis-by-environment interaction was not. Utilization of the known major QTLs for heading date in breeding through gene pyramiding needs take epistasis into consideration.

Heterotic loci for various morphological traits of maize detected using a single segment substitution lines test-cross population

Heterosis has been exploited to increase grain yield, quality, and resistance in many crops, and it plays an important role in plant breeding. However, the genetic mechanism of heterosis remains unclear. To dissect the genetic basis of heterosis, a set of 203 single segment substitution lines (SSSLs) was developed, and its test-cross population was used to identify heterotic loci (HL) for plant morphological traits in maize, including plant height (PH), ear height (EH), leaf number (LN), tassel main axis length (TMAL), and tassel branch number (TBN). A total of 41 QTLs and 37 HL were identified for five morphological traits in the test-cross population derived from the 203 SSSLs and the parent, Xu178. Nine HL for PH, nine HL for EH, seven HL for LN, seven HL for TMAL, and five HL for TBN were detected in three different environments, respectively. Eight HL, ph1a, ph1b, ph2, ph5, eh3a, eh3b, eh10, and tmal1b, were simultaneously detected in the three environments. Among the 37 HL, only 10 (27.03 %; for PH, EH, LN, and TBN) had a corresponding QTL (24.39 %) sharing the same chromosomal region. Of all the HL, 21.4 % showed dominance effects, 76.8 % showed over-dominance effects, and only one (1.8 %) showed a partial-dominance effect. This result illustrated that heterosis and performance was controlled by different genetic mechanisms, and over-dominance effects were the main contributors to heterosis for plant-related traits at the single-locus level in maize.

Comparison of amylopectin structure and activities of key starch synthesis enzymes in the grains of rice single-segment substitution lines with different Wx alleles

The Wx gene is the major gene controlling amylose synthesis in rice endosperm. So far, the Wx gene can be mainly classified into five common alleles, wx, Wx t, Wx g1, Wx g2, and Wx g3, according to their amylose phenotypes. Besides, the Wx allelic variation was also found to play an important role in regulating other physicochemical properties of rice starch. However, the specific physiological and starch structural mechanisms are not clear yet. With a set of single-segment substitution lines harboring five different Wx alleles, the genotype differences in amylopectin structure and dynamic changes of activities of key starch synthesis enzymes were investigated. The distinct Wx genotype difference in chain length distribution of amylopectin was confirmed by size exclusion chromatography. There were clear allelic differences in activities of starch synthesis enzymes during grain filling. The Wx allelic variation had the highest impact on the activities of starch branching enzyme, followed by pullulanase, and soluble starch synthase, while no influence on isoamylase activity. Differences in structural features of amylopectin and mean enzyme activities during grain filling period correlated well with most of the variations in starch property traits. These findings indicate that the Wx allelic variation may affect starch structure and physicochemical properties through selectively influencing activities of starch synthesis enzymes in developing rice grains. The present results will contribute to our understanding of the regulation of starch biosynthesis in rice endosperm.

Development of a platform for breeding by design of CMS lines based on an SSSL library in rice (Oryza sativa L.)

Cytoplasmic male sterility (CMS) is an important foundation for heterosis utilization and exploited widely to hybrid seed production in rice. However, the traditional experience-driven and labor-cost breeding style left little room for sustainable improvement of hybrid rice. Here, we report a platform for breeding by design of CMS lines based on an SSSL library. A line H121B with rf3 and rf4 genes from XieqingzaoB was first developed in the Huajingxian74 (HJX74) genetic background. Using H121B as maintainer line, three isonuclear alloplasmic CMS lines, W-H121A, D-H121A and Y-H121A, with the wild abortive, dwarf wild abortive, and Yegong abortive types of CMS cytoplasm, respectively, were developed. The H121B maintainer line was then improved by a way of breeding by design. Three target genes, gs3 for long grain, Wx t for low amylose content, and OsMADS50 for early heading date, in the chromosomal substituted segments of single segment substitution lines were selected from the SSSL library in the HJX74 genetic background, and were pyramided together in H121B through marker-assisted selection. The new maintainer line, H131B, showing the phenotypes of longer in grain length, lower in amylose content, and earlier in heading date than those in H121B, achieved the breeding goal designed. Using H131B as maintainer line, three new isonuclear alloplasmic CMS lines, W-H131A, D-H131A and Y-H131A, were developed. Establishment of the platform for breeding by design of CMS lines will be helpful for sustainable improvement of CMS lines in hybrid rice development.

Detection and characterization of epistasis between QTLs on plant height in rice using single segment substitution lines.

Hua-jing-xian 74 and its 12 single segment substitution lines (SSSLs) in rice were used as crossing parents to construct a half diallel crossing population. A total number of 91 materials were grown under three planting densities. By analysis of average plant height (PH) over all environments 10 SSSLs were detected with significant additives and 6 SSSLs with significant dominances. These SSSLs were further tested under different densities respectively, indicating that some of single locus effects were sensitive to densities and the conditions under the density of 16.7 cm × 16.7 cm maybe inhibited the expressing of these PH QTLs. Qualitative and quantitative analyses of each four participating genotypes indicated that digenic interactions among these QTLs were prevalent. Of 66 tested interactions, about 42.4% were epistatic (P < 5%). Although some QTLs hadn’t single locus effects, they were possible to form digenic interactions. A significant finding was that the detected epistases were mostly negative. Additionally, these epistases were also found being sensitive to planting densities, the conditions under the density of 10 cm × 16.7 cm perhaps promoted the expressing of epistatic interactions among PH QTLs.

QTL Detection and Epistasis Analysis for Heading Date Using Single Segment Substitution Lines in Rice (Oryza sativa L.)

Heading date of rice is a key agronomic trait determining cultivated areas and seasons and affecting yield. In the present study, five primary single segment substitution lines with the same genetic background were used to detect quantitative trait loci (QTLs) for heading date in rice. Two QTLs, qHD3 and qHD6 on the short arm of chromosome 3 and the short arm of chromosome 6, respectively, were identified under natural long-day (NLD). Nineteen secondary single segment substitution lines (SSSLs) and seven double segments pyramiding lines were designed to map the two QTLs and to evaluate their epistatic interaction between them. By overlapping mapping, qHD3 was mapped in a 791-kb interval between SSR markers RM3894 and RM569 and qHD6 in a 1125-kb interval between RM587 and RM225. Results revealed the existence of epistatic interaction between qHD3 and qHD6 under natural long-day (NLD). It was also found that qHD3 and qHD6 had significant effects on plant height and yield traits, indicating that both of the QTLs have pleiotropic effects.

The novel methods of development of the maintainer and cytoplasmic male sterile lines with different cytoplasms based on chromosome single-segment substitution lines in rice

The present study was carried out with the objective of developing new parental lines of hybrid rice based on chromosome single-segment substitution lines (SSSLs), on which the restorer and maintainer genes Rf3 (rf3) and Rf4 (rf4) were harbored in rice. To develop the new 3-line hybrid, the SSSL W23-19-06-06-11 with the genotype Rf3Rf3/Rf4Rf4 [a strong restorer line for wild abortive (WA), dwarf-wild abortive (DA), and Yegong (Y) cytoplasmic male sterile (CMS) lines] was crossed 4 times as the male parent with 4 CMS lines: 2 typical WA-type CMS lines of Bobai A and Zhenshan 97A, 1 typical Y-type CMS line of Y-Huanong A, and 1 typical DA-type CMS line of Xieqingzao A. In the BC_3F_2 populations, the male sterile plants (MSPs) with WA-, Y-, and DA-type CMS sources and nuclear background of W23-19-06-06-11 and their maintainer plants (MPs) were developed by backcrossing and marker-assisted selection. All the MSPs showed 100% pollen and spikelet sterility and the panicle length ranged from 20 to 22.6 cm. The extent of incomplete panicle exertion in the entries ranged from -40.7 to -48.5. The pollen grain viability assay with I_2KI of the MSPs revealed 100% pollen sterility, consisting of both typical and spherical abortive pollen grains. The MPs showed normal pollen (spikelet) fertility. A genome-wide DNA marker survey revealed that the numbers of the substituted chromosome segments carried by the MSPs and MPs were 0.8 and 0.6, while the lengths of the substituted chromosome segments corresponding to the Rf3 (or Rf4) locus were, on average, 26.2 cM and 17.0 cM (or 15.3 cM and 15.1 cM).