Single Segment Substitution Lines Research Articles

QTLs detection and pyramiding for stigma exsertion rate in wild rice species by using the single-segment substitution lines

QTLs detection and pyramiding for stigma exsertion rate in wild rice species by using the single-segment substitution lines

Analysis of QTL for Grain Size in a Rice Chromosome Segment Substitution Line Z1392 with Long Grains and Fine Mapping of qGL-6

BackgroundGrain size affects not only rice yield but is also an important element in quality of appearance. However, the mechanism for inheritance of grain size is unclear.ResultsA rice chromosome segment substitution line Z1392, which harbors three substitution segments and produces grains of increased length, was identified. The three chromosome segments were located on chromosomes 1, 5, and 6, and the average length of the substitution segment was 3.17 Mb. Cytological analysis indicates that the predominant cause of increased grain length in Z1392 could be cell expansion in the glumes. Seven quantitative trait loci (QTLs) for grain size related traits were identified using the secondary F2 population produced by Nipponbare/Z1392. The inheritance of grain length in Z1392 was mainly controlled by two major QTLs, qGL-5 and qGL-6. qGL-6 was localized on a 1.26 Mb region on chromosome 6, and OsARF19 may be its candidate gene. Based on QTL mapping, three single-segment substitution lines (S1, S2, and S3) and two double-segment substitution lines (D1 and D2) were selected, and the mapping accuracy for qGL-5 and qGL-6 was further verified using three single-segment substitution lines. Analysis of QTL additive and epistatic effects revealed that the additive effect of alleles qGL-5 and qGL-6 from ‘Xihui 18’ was estimated to increase grain length of Z1392 by 0.22 and 0.15 mm, respectively. In addition, a positive epistatic interaction between qGL-5 and qGL-6 was detected, which indicates that the pyramiding of qGL-5 and qGL-6 for grain length produces a novel genotype with longer grains.ConclusionsInheritance of grain length in the triple-segment substitution line Z1392 is mainly controlled by two major QTLs, qGL-5 and qGL-6. qGL-6 was found to be located in a 1.26 Mb region on chromosome 6, and OsARF19 may be its candidate gene. A positive epistatic interaction between qGL-5 and qGL-6 results in longer grains. The present results can be used to facilitate cloning of the qGL-5 and qGL-6 genes and contribute to improvement of grain yield in rice.

Substitution Mapping of the Major Quantitative Trait Loci Controlling Stigma Exsertion Rate from Oryza glumaepatula

BackgroundStigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula, a wild Oryza species.ResultsSeven QTLs for SER were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an estimated interval of 898.8 kb by secondary substitution mapping. qSER-5, qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to an estimated region of 551.9 kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, which were higher than those of most loci for SER reported previously.ConclusionsqSER-1a and qSER-1b are novel loci for SER on chromosome 1. All of the 7 QTLs have major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.

Identification of long-grain chromosome segment substitution line Z744 and QTL analysis for agronomic traits in rice

Length of grain affects the appearance, quality, and yield of rice. A rice long-grain chromosome segment substitution line Z744, with Nipponbare as the recipient parent and Xihui 18 as the donor parent, was identified. Z744 contains a total of six substitution segments distributed on chromosomes (Chrs.) 1, 2, 6, 7, and 12, with an average substitution length of 2.72 Mb. The grain length, ratio of length to width, and 1 000-grain weight of Z744 were significantly higher than those in Nipponbare. The plant height, panicle number, and seed-set ratio in Z744 were significantly lower than those in Nipponbare, but they were still 78.7 cm, 13.5 per plant, and 86.49%, respectively. Furthermore, eight QTLs of different traits were identified in the secondary F2 population, constructed by Nipponbare and Z744 hybridization. The grain weight of Z744 was controlled by two synergistic QTLs (qGWT1 and qGWT7) and two subtractive QTLs (qGWT2 and qGWT6), respectively. The increase in the grain weight of Z744 was caused mainly by the increase in grain length. Two QTLs were detected, qGL1 and qGL7-3, which accounted for 25.54 and 15.58% of phenotypic variation, respectively. A Chi-square test showed that the long-grain number and the short-grain number were in accordance with the 3:1 separation ratio, which indicates that the long grain is dominant over the short-grain and Z744 was controlled mainly by the principal effect qGL1. These results offered a good basis for further fine mapping of qGL1 and further dissection of other QTLs into single-segment substitution lines.

Identification of MicroRNAs and Their Targets That Respond to Powdery Mildew Infection in Cucumber by Small RNA and Degradome Sequencing.

Powdery mildew (PM) is a prevalent disease known to limit cucumber production worldwide. MicroRNAs (miRNAs) are single-stranded molecules that regulate host defense responses through posttranscriptional gene regulation. However, which specific miRNAs are involved and how they regulate cucumber PM resistance remain elusive. A PM-resistant single-segment substitution line, SSSL508-28, was developed previously using marker-assisted backcrossing of the PM-susceptible cucumber inbred D8 line. In this study, we applied small RNA and degradome sequencing to identify PM-responsive miRNAs and their target genes in the D8 and SSSL508-28 lines. The deep sequencing resulted in the identification of 156 known and 147 novel miRNAs. Among them, 32 and six differentially expressed miRNAs (DEMs) were detected in D8 and SSSL508-28, respectively. The positive correlation between DEMs measured by small RNA sequencing and stem-loop quantitative real-time reverse transcription–polymerase chain reaction confirmed the accuracy of the observed miRNA abundances. The 32 DEMs identified in the PM-susceptible D8 were all upregulated, whereas four of the six DEMs identified in the PM-resistant SSSL508-28 were downregulated. Using in silico and degradome sequencing approaches, 517 and 20 target genes were predicted for the D8 and SSSL508-28 DEMs, respectively. Comparison of the DEM expression profiles with the corresponding mRNA expression profiles obtained in a previous study with the same experimental design identified 60 and three target genes in D8 and SSSL508-28, respectively, which exhibited inverse expression patterns with their respective miRNAs. In particular, five DEMs were located in the substituted segment that contained two upregulated DEMs, Csa-miR172c-3p and Csa-miR395a-3p, in D8 and two downregulated DEMs, Csa-miR395d-3p and Csa-miR398b-3p, in SSSL508-28. One gene encoding L-aspartate oxidase, which was targeted by Csa-miR162a, was also located on the same segment and was specifically downregulated in PM-inoculated D8 leaves. Our results will facilitate the future use of miRNAs in breeding cucumber varieties with enhanced resistance to PM.

Heterotic loci analysis for root traits of maize seedlings using an SSSL test population under different nitrogen conditions

Exploitation of heterosis is an efficient strategy to increase crop production, improve quality, and enhance resistance to biotic and abiotic stresses. However, heterosis shows significant genetic × environment effects. Nitrogen is an important nutrient that affects crop development and grain yield. Hybrid maize performs significantly and differently depending on the nitrogen conditions, but the genetic basis of maize heterosis under different nitrogen conditions is unclear. In this study, a test population comprising a set of single segment substitution lines (SSSLs) was used to identify heterotic loci (HL) for root-related traits of maize seedlings under two nitrogen conditions. We identified 80 HL for the root system and related traits in maize seedlings, consisting of 16, 18, 10, 11, 11, and 14 HL associated with root length (RL), root surface area (RSA), root average diameter (RAD), shoot dry weight (SDW), root dry weight (RDW), and plant height (PH), respectively. Among them, 13% of the HL were detected under both nitrogen conditions simultaneously, including the HLs hRL1b, hRL7, hRL9, hRSA7a, hRSA9a, hRAD1a, hSDW6, hSDW7a, hSDW7b, and hPH6a, but most of the HLs (87%) were not detected under both nitrogen conditions. The results indicated that, in maize, heterosis also exists in the interaction between genotype and nitrogen level.

Characterization and fine-mapping of qHd2-1, a minor quantitative locus that affects heading date under long-day conditions in rice (Oryza sativa L.)

Heading date, a complex quantitative trait, determines regional adaptability and is associated with grain yield and quality in rice. In this study, we characterized qHd2-1, a minor-effect quantitative locus (QTL) for promoting heading date (by 3–4 days) under long-day (LD) conditions, but not short-day (SD) conditions. The qHd2-1 locus was detected in single segment substitution line (SSSL) N22-1, which was developed using indica 9311 as the donor and japonica Nipponbare (NP) as the recipient. A set of substitution lines were developed from a segregating population derived from a cross between N22-1 and NP. Based on the genotypic identification and phenotypic evaluation of the target substitution lines, qHd2-1 was narrowed down to a 105-kb region between STS2-20 and STS2-22 on the short arm of chromosome 2. Furthermore, qHd2-1 was found to function by upregulating the florigen genes Hd3a and RFT1 during floral induction under LD conditions. Field tests showed that qHd2-1 promotion of heading date affects grain yield‑related agronomic traits, such as plant height, panicle number per plant, and flag leaf size, as well as thousand-grain weight and grain width. Taken together, these findings establish a foundation for cloning this minor-effect QTL involved in heading date, and qHd2-1 could be of great significance in rice breeding to allow the fine-tuning of heading date in rice cultivars.

Comparative proteomic analysis of cucumber powdery mildew resistance between a single-segment substitution line and its recurrent parent

Powdery mildew (PM) is considered a major cause of yield losses and reduced quality in cucumber worldwide, but the molecular basis of PM resistance remains poorly understood. A segment substitution line, namely, SSL508-28, was developed with dominant PM resistance in the genetic background of PM-susceptible cucumber inbred line D8. The substituted segment contains 860 genes. An iTRAQ-based comparative proteomic technology was used to map the proteomes of PM-inoculated and untreated (control) D8 and SSL508-28. The number of differentially regulated proteins (DRPs) in SSL508-28 was almost three times higher than that in D8. Fourteen DRPs were located in the substituted segment interval. Comparative gene expression analysis revealed that nodulin-related protein 1 (NRP1) may be a good candidate for PM resistance. Gene Ontology enrichment analysis showed that DRPs functioning in tetrapyrrole biosynthetic process, sulfur metabolic process and cell redox homeostasis were specifically enriched in the resistant line SSL508-28. DRPs categorized in the KEGG term photosynthesis increased in both lines upon PM infection, suggesting that the strategies used by cucumber may be different from those used by other crops to react to PM attacks at the initial stage. The measurement of hydrogen peroxide and superoxide anion production and net photosynthetic rate were consistent with the changes in protein abundance, suggesting that the proteomic results were reliable. There was a poor correlation between DRPs measured by iTRAQ and the corresponding gene expression changes measured by RNA-seq with the same experimental design. Taken together, these findings improve the understanding of the molecular mechanisms underlying the response of cucumber to PM infection.

Natural variation at OsCERK1 regulates arbuscular mycorrhizal symbiosis in rice.

The symbiotic interaction between arbuscular mycorrhizal fungi (AMF) and land plants is essential for efficient nutrient acquisition and utilisation. Our understanding of key processes controlling the AMF colonisation in rice is still limited. Dongxiang wild rice (DY) exhibited a stronger colonisation with Rhizophagus irregularis than the rice cultivar Zhongzao 35 (ZZ35). Chromosome segment substitution lines were constructed and the OsCERK1 gene from DY was mapped. Transgenic plants in the japonica rice Zhonghua 11 (ZZ11) were constructed to compare root colonisation by AMF. Chromosome single-segment substitution lines containing OsCERK1DY showed higher phosphorus content and grain yield relative to ZZ35. Four amino acids substitutions were identified among the OsCERK1 haplotypes of DY, ZZ35 and ZH11 and two of these were in the second lysine-motif domain, which is essential for the differences of AMF colonisation level among rice varieties. Heterologous expression of OsCERK1DY in ZH11 significantly enhanced AMF colonisation and increased resistance against the pathogenic fungi Magnaporthe oryzae. Notably, the OsCERK1DY haplotype was absent from 4660 cultivated rice varieties. We conclude that OsCERK1 is a key gene affecting the symbiotic interaction with AMF and OsCERK1DY has the biotechnological potential to increase rice phosphorus acquisition and utilisation efficiency for sustainable agriculture.

Identification of rice chromosome segment substitution Line Z747 with increased grain number and QTL mapping for related traits

Increasing grain number per panicle is important for rice breeding for high yield. Its inheritance is very complex and controlled by many genes. Chromosome segment substitution lines can dissect complex traits controlled by many genes, and thus are ideal genetic research materials. Here, an excellent rice chromosome segment substitution line Z747 with increased grain number was identified from recipient Nipponbare and donor Xihui 18 through advanced backcrossing and inbreeding combined SSR marker-assisted selection. Z747 carried fifteen substitution segments with 4.49 Mb of average length. Compared with Nipponbare, Z747 had significantly increased spikelet number per panicle, number of primary branches, number of secondary branches, panicle length and grain length, and decreased grain width and seed setting rate. However, the seed setting rate in Z747 was still up to 81%. Furthermore, secondary F2 population from crosses between Nipponbare and Z747 was used to map QTL for related traits. A total of 46 QTLs distributed on chromosomes 1, 2, 3, 5, 6, 9, 11, and 12 were detected. Among them, 12 QTLs such as qGPP12 , qPH-3-1 , and qPH-3-2 etc. might be alleles of cloned genes, and the remaining 34 QTLs such as qSPP9 etc. might not be identified in the past. The spikelet number per panicle of Z747 was mainly controlled by two QTLs ( qSPP3 and qSPP5 ) with effects of increasing spikelet number and one ( qSPP9 ) with decreasing effects. These results are important for fine mapping and cloning of major QTL, and developing single-segment substitution lines carrying favorable QTLs.

Breeding by design of CMS lines on the platform of SSSL library in rice

Greatly increased yield by utilizing of heterosis has been a great success in rice over the past 40 years. The cytoplasmic male sterility (CMS) line is a key line of hybrid rice. However, the CMS line was very difficult to develop following the traditional breeding methods. Here, we report an example to develop and improve CMS lines sustainably by using the strategy of breeding by design under the platform of single segment substitution line (SSSL) library in the Huajingxian74 (HJX74) genetic background. The CMS lines HZA and HBA with the wild abortive (WA) cytoplasm from Zhenshan97A and BobaiA, respectively, were firstly developed in the HJX74 background through marker-assisted selection. Then, four isonuclear alloplasmic CMS lines with the WA, dwarf wild abortive (DA), and Yegong abortive (YA) types of CMS cytoplasm, respectively, were developed by using the HZB maintainer line. According to the goal of design, E5-HXA and E5-HBA were developed by pyramiding five target genes, Wxg1, ALK, fgr, gs3, and OsMADS50, located on the chromosomal substituted segments in four SSSLs. The two CMS lines show the phenotypes of earlier in heading date, longer and narrower in grain shape, lower in amylose content, and fragrant smell. Thus, the goal of design was achieved on the platform of SSSL library. Compared with that in the E5-HXA line carrying the rf3 and rf4 genes of XieqingzaoA, the CMS in the E5-HBA line with the rf3 and rf4 genes from BobaiA was susceptible to environmental impact and easy to be restored. Therefore, the balance between sterility and its restored ability in CMS lines should be concerned in breeding by design.

The platform of breeding by design based on the SSSL library in rice

Breeding by design is a new concept proposed in the beginning of the century. It refers to the breeding of varieties by crop design utilizing favorable alleles dispersed in different genetic resources in a genome. In the past 20 years, we have proposed a "three-step" strategy to carry out the research on breeding by design in rice. Firstly, we constructed a library of chromosomal single-segment substitution lines (SSSLs) by using of Huajingxian74 (HJX74), an elite xian (indica) variety from South China as the recipient and 43 accessions of seven species of rice AA genome as donors. The genes in the substituted segments of SSSLs were then detected. Breeding by design was conducted by selecting the favorable genes from the SSSL library. Our practice indicates that the SSSL library is a powerful platform for breeding by design and various "traits", "lines" and "varieties" of rice can be designed and bred by utilizing abundant genes in the SSSL library. Here, we introduce the platform of the HJX74-SSSL library and our work of breeding by design on the platform. It will provide a case study for crop design.

Fine mapping and candidate gene analysis of qhkw5-3, a major QTL for kernel weight in maize.

KEY MESSAGE: qhkw5-3, a major QTL for kernel weight in maize, was mapped to an interval of 125.3kb between the InDel markers InYM20 and InYM36, and the candidate genes were analysed. Yield, of which kernel weight is a major component, is the primary trait of interest in maize breeding programmes. In our previous study, a major QTL (named qhkw5-3), which controls hundred-kernel weight, was identified and mapped to the interval between simple sequence repeat (SSR) markers SYM033 and SYM108 on chromosome 5, using an F2:3 population derived from a cross between the maize inbred line Zheng58 and the single-segment substitution line Z22. In order to fine map qhkw5-3, a larger BC1F1 segregating population of 14,759 seeds, derived from a (Z22 × Zheng58) × Z22 cross, was screened using the SSR markers SYM036 and SYM119. Forty genotypes with donor chromosomal fragments of different lengths were obtained. Progeny testing results indicated that qhkw5-3 was mapped to an interval of 442.6kb between the SSR markers SYM077 and SYM084. Overlap mapping results, based on seven homozygous recombinant lines, showed that qhkw5-3 was narrowed down to an interval of 125.3kb between the InDel markers InYM20 and InYM36. Within this interval, six candidate genes were analysed using qRT-PCR. The results of this study lay the foundations for cloning and functional analysis of qhkw5-3 and will contribute to advancing our knowledge of the genetic basis of yield traits in maize.

Genetic characterization of the chromosome single-segment substitution lines of O. glumaepatula and O. barthii and identification of QTLs for yield-related traits

Oryza glumaepatula and Oryza barthii are AA-genome wild species in Oryza genus. In order to effectively mine and transfer beneficial genes from these wild species in genome-wide by distant hybridization, in the present study, the chromosome single-segment substitution lines (SSSLs) were developed using O. glumaepatula and O. barthii as donors and elite indica cultivar, HJX74, as a recipient. A total of 168 homozygous SSSLs of O. glumaepatula (GLU-SSSLs) and 95 homozygous SSSLs of O. barthii (BAR-SSSLs) were developed. In 168 GLU-SSSLs and 95 BAR-SSSLs, the total lengths of the substituted segments distributing on 12 chromosomes were 3636.35 cM and 1731.65 cM, respectively. Accordingly, the mean length of each substituted segment was 21.64 cM in GLU-SSSLs and 18.23 cM in BAR-SSSLs. The total coverage lengths of the substituted segments on rice genome were 80.15% in GLU-SSSLs and 54.67% in BAR-SSSLs. To evaluate the utilization potential of these SSSLs, four yield-related traits, heading date, plant height, seed-setting rate, and 1000-grain weight, were investigated in the SSSLs over two seasons. Significant variations of the traits were observed among the SSSLs. At P ≤ 0.05 level, a sum of 28 stable QTLs in GLU-SSSLs and 53 in BAR-SSSLs were identified. Among them, the additive effects of 12 QTLs contributed averagely more than 10% for phenotypic variations, viz., qPHg1-2, qGWTg9-2, qHDb1-1, qPHb1-2, qPHb1-3, qPHb7-1, qPHb7-2, qPHb8-1, qPHb10-1, qPHb12-2, qSSb7-1, and qSSb10-2. Nine pairs of QTLs in the two donors were comparatively mapped on chromosomes 1, 5, and 10, which means the same QTLs or alleles existing in O. glumaepatula and O. barthii have been detected and transferred to SSSLs. Besides, qGWTg1-1, qGWTg4-1, and qGWTb1-1 have shown positive additive effects, implying alleles from the two wild donors of these QTLs have the potential in increasing 1000-grain weight in SSSLs. The SSSLs library of the wild species is a valuable resource for rice germplasm innovation and breeding.

Map-based cloning of a new total loss-of-function allele of OsHMA3 causes high cadmium accumulation in rice grain.

Rice (Oryza sativa) is a major dietary source of the toxic metal cadmium (Cd). Reducing Cd transfer from soil to the rice grain is important for food safety. Rice cultivars vary widely in their Cd accumulation, but the genetic basis for this variation is not fully understood. Based on field and pot experiments comparing 26 rice cultivars, we identified a cultivar with high Cd accumulation in grain (BG367, coded as W4) and a cultivar with low grain Cd accumulation (Huajingxian 74, coded as W0). W4 showed a higher Cd translocation from roots to shoots than W0. Using chromosome single segment substitution lines derived from the two cultivars, we mapped a quantitative trait locus for Cd accumulation in grain to a 400 kb region in chromosome 7. Using yeast expression assays and transgenic complementation, we identified OsHMA3 as the causal gene at this locus. Compared with OsHMA3W0, OsHMA3W4 has a deletion of 14 amino acids predicted to be in the ATP binding domain. OsHMA3W4 showed a complete loss of transport activity for Cd in yeast assays. Taking our findings together, we have identified a new allele of OsHMA3 with a total loss-of-function, resulting in greatly elevated Cd translocation to rice shoots and grain.

Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

AbstractPanicle length (PL), an important yield‐related trait, strongly affects yield components, such as grain number, grain density and rice quality. More than 200 panicle length quantitative trait loci (PL QTLs) are identified, but only a small number are applied in rice breeding. In this study, we performed QTL analysis for PL using 42 single‐segment substitution lines (SSSLs) derived from nine donors in the genetic background of HJX74. Fourteen QTLs and five heterosis QTLs (HQTLs) for PL were recognised. Three QTLs and four HQTLs acted positively, and the other eleven QTLs and one HQTL acted negatively. By scanning the single heterozygous background region of the F2 population with large‐genetic‐effect SSSLs, we mapped PL loci qPL6‐2 and qPL7‐1 to different locations on chromosomes 6 and 7, respectively, in three consecutive years of independent trials. The genetic effects of these QTLs were further assessed. qPL6‐2 demonstrated the most positive additive effect (QTL), whereas qPL7‐1 achieved the most positive dominant effect (HQTL) for PL. These results indicated that the pyramiding of PL QTLs might increase grain yield and facilitate the application of the beneficial allele in hybrid rice breeding.

Identification and QTL mapping of Z550, a rice backcrossed inbred line with increased grains per panicle

An elite backcrossed inbred line Z550 with increased grains per panicle was identified from advanced backcrosses between Nipponbare and Xihui 18 by simple sequence repeat (SSR) marker-assisted selection (MAS). Z550 carries 13 substitution segments distributed on chromosomes 1, 6, 7, 8, 9, 10, and 12, with an average substitution length of 1.68 Mb. Compared with the Nipponbare parental line, plant height, panicle length, spikelets per panicle, grains per panicle, and grain weight for Z550 were significantly increased. While the grain width of Z550 was significantly narrower, and the seed setting ratio (81.43%) was significantly lower than that of Nipponbare, it is still sufficient for breeding purposes. Quantitative trait loci (QTLs) mapping for important agronomic traits was conducted with the F2 population derived from Nipponbare crossed with Z550 using the restricted maximum likelihood (REML) method. A total of 16, including 12 previously unreported QTLs were detected, with contribution rates ranging from 1.46 to 10.49%. Grains per panicle was controlled by 8 QTLs, 5 of which increased number of grains whereas 3 decreased it. qGPP-1, with the largest contribution (10.49%), was estimated to increase grains per panicle by 30.67, while qGPP-9, with the minimum contribution rate (2.47%), had an effect of increasing grains per panicle by 15.79. These results will be useful for further development of single segment substitution lines with major QTLs, and for research of their molecular functions via QTL cloning.

Identification of S23 causing both interspecific hybrid male sterility and environment-conditioned male sterility in rice

BackgroundOryza glumaepatula represents an important resource of genetic diversity that can be used to improve rice production. However, hybrid sterility severely restricts gene flow between Oryza species, and hinders the utilization of distant heterosis in hybrid rice breeding.ResultsIn order to fully exploit the beneficial genes of O. glumaepatula and facilitate the conservation of these gene resources, a set of chromosome single-segment substitution lines (SSSLs) was developed using an indica variety HJX74 as the recurrent parent and an accession of O. glumaepatula as the donor parent. During the process of SSSLs development, S23, a locus conferring hybrid male sterility between O. sativa and O. glumaepatula, was identified and fine mapped to 11.54 kb and 7.08 kb genomic region in O. sativa and O. glumaepatula, respectively, encoding three and two candidate ORFs, respectively. qRT-PCR and sequence analysis excluded one common ORF as the candidate gene. In addition, hybrid male sterility caused by S23 was environment-sensitive, and could be observed only in natural short-day (NSD).ConclusionIdentification and candidate genes analysis of S23 in this study provides a valuable example to study the crosstalk between interspecific F1 hybrid male sterility and environment-conditioned male sterility in rice, facilitates reserving and utilizing favorable genes or alleles of wild Oryza species, and allows for a more efficient exploitation of distant heterosis in hybrid rice breeding.

Analysis of QTLs on heading date based on single segment substitution lines in rice (Oryza Sativa L.)

Single segment substitution lines (SSSLs) have been confirmed to be powerful tools to perform quantitative trait locus (QTL) analysis. This study illuminated the process and methods of QTL analysis with SSSLs on heading date (HD) in rice. QTL identification under two cropping seasons revealed 98 of 202 SSSLs associated with HD. A total of 22 QTLs were positioned in relative narrow regions on chromosomes by mrMLM.GUI software. QTL qHd3-1 was precisely positioned at 4.4 cM on chromosome 3 by a secondary F2 population. Through SSSL pyramiding, double segment substitution lines were constructed and used to analyze epistatic interactions of digenic loci. Epistatic effects for three pairs of QTLs were estimated, indicating the interactions of QTL qHd3-1 with other QTLs detected and the role to enhance the expression of early ripening or restraining of late flowering QTLs. Additionally, analysis of QTL in different environments provided information about the stability of HD QTLs. This type of research points out the way to excavate favorable genes for design breeding.

Mapping of Hd-6-2 for Heading Date Using Two Secondary Segregation Populations in Rice

Abstract: Heading date is one of the most important traits for rice adaption to different cultivation areas and crop seasons. In this study, two single segment substitution lines (SSSLs), W31-41-61-3-11-3-6-7 (W31-SSSL) and W32-59-80-2-11-1-10 (W32-SSSL) with substituted intervals derived from the donor parents IR66897B (W31) and IR66167-27-5-1-6 (W32), respectively, with Huajingxian 74 (HTX74) were found to comprise a gene for extremely late-heading date, and the gene was tentatively designated as Hd-6-2. Two secondary F2 segregating populations were developed by crossing the two heterozygous SSSLs with HJX74 to map Hd-6-2 gene. According to phenotype analysis of the two mapping populations, the late heading date trait was controlled by a major recessive gene. In the segregation population derived from W31-SSSL, Hd-6-2 was mapped on chromosome 6 between PSM677 and RM204 with the genetic distances of 1.3 and 2.7 cM, respectively. In the population of W32-SSSL, the gene for heading date was mapped to the similar region as Hd-6-2 and co-segregated with PSM672. The sequence alignment of Hd3a in the coding domains and promoter regions of HJX74 and W31-SSSL are completely consistent, whereas there was a great difference between W32-SSSL and HJX74, suggesting that Hd3a could hardly be the main cause of the heading date variation in W31-SSSL, but it was probably the main reason for the change of heading stage in W32-SSSL.