Chromosomal Interval Research Articles

Whole-genome mining of abiotic stress gene loci in rice.

We projected meta-QTL (MQTL) for drought, salinity, cold state, and high metal ion tolerance in rice using a meta-analysis based on high-density consensus maps. In addition, a genome-wide association analysis was used to validate the results of the meta-analysis, and four new chromosome intervals for mining abiotic stress candidate genes were obtained. Drought, severe cold, high salinity, and high metallic ion concentrations severely restrict rice production. Consequently, the breeding of abiotic stress-tolerant variety is being paid increasingly more attention. This study aimed to identify meta-quantitative trait loci (MQTL) for abiotic stress tolerance in rice, as well as the molecular markers and potential candidate genes of the MQTL regions. We summarized 2785 rice QTL and conducted a meta-analysis of 159 studies. We found 82 drought tolerance (DT), 70 cold tolerance (CT), 70 salt tolerance (ST), and 51 heavy metal ion tolerance (IT) meta-QTL, as well as 20 DT, 11 CT, 22 ST, and 5 IT candidate genes in the MQTL interval. Thirty-one multiple-tolerance related MQTL regions, which were highly enriched, were also detected, and 13 candidate genes related to multiple-tolerance were obtained. In addition, the correlation between DT, CT, and ST was significant in the rice genome. Four candidate genes and four MM-QTL regions were detected simultaneously by GWAS and meta-analysis. The four candidate genes showed distinct genetic differentiation and substantial genetic distance between indica and japonica rice, and the four MM-QTL are potential intervals for mining abiotic stress-related candidate genes. The candidate genes identified in this study will not only be useful for marker-assisted selection and pyramiding but will also accelerate the fine mapping and cloning of the candidate genes associated with abiotic stress-tolerance mechanisms in rice.

Identification of candidate gene for resistance to broomrape (Orobanche cumana) in sunflower by BSA-seq

Broomrape (Orobanche cumana) is one of the most important parasitic plants that drastically reduces sunflower yield. The majority of existing resistance varieties have become insufficient for crop protection. Breeding for broomrape resistance is regarded as the most effective and environmentally friendly control measure. In this paper, mapping of a resistance gene for broomrape races E was performed in a recombinant inbred line population by bulk segregate analyses (BSA) combined with genotyping by-sequencing technology. One QTL with resistance candidate genes was mapped on 5 ​kb interval location from 157,393,001 to 157,850,000 on chromosome 3, the other QTL was located at 5,000 bp interval location from 173,910,001 to 173,915,000 on chromosome 14. Genomic region on candidate interval of chromosome 3 revealed 6 genes with potential resistance for broomrape including transcription factor MYB1R1, Phylloplanin, histone-lysine N-methyltransferase, methylglutaconyl-CoA hydratase, fasciclin-like arabinogalactan protein and fatty acid dehydrogenase. Two resistant genes on candidate interval of chromosome 14 were discovered with potential resistance for broomrape, which were ABC transporter C family member and Ethylene-responsive transcription factor. These precise locations would be valuable for selecting resistant genotypes in future.

Identification and mapping of quantitative trait loci (QTL) and epistatic QTL for salinity tolerance at seedling stage in traditional aromatic short grain rice landrace Kolajoha (Oryza sativa L.) of Assam, India

Salinity stress is the most prominent stress impacting rice productivity worldwide. In the past, several quantitative trait loci (QTLs) for salinity tolerance had been identified in rice, however their utilization in rice breeding programs is largely confounded due to the unwanted linkage drag associated with the QTL region. Thus, it is strongly desirable to delimit the QTL region to a least possible chromosomal interval minimising any unwanted association. Addressing this, we have evaluated 68 recombinant inbred lines (RILs) derived from a cross between a salinity tolerant parent ‘Kolajoha’ and a salinity sensitive parent ‘Ranjit’ for identification of QTL(s) involved in imparting salinity tolerance at seedling stage. Genotyping by sequencing approach (GBS) was followed for SNP identification at genome wide scale. Around 3649 SNPs were identified by GBS method initially at 20% minor allele frequency. After filtering of SNPs with polymorphism with less than 10–15% of missing data, a total of 1248 SNPs were mapped to 1247 recombination points and the genetic map was constructed with a total map length of 1201.21 cM and resolution of 0.95 cM between markers. For 10 traits, a total of 23 additive QTLs were identified of which only 1 was a major QTL and 22 were minor QTLs. The average QTL interval size is about 2945 kb. Epistatic QTL mapping had identified one pair of QTLs that contribute significantly in the phenotypic variation of traits among the RILs. Total 1895 genes were identified in the QTL intervals, majority of them are located in Chr1 of rice genome between 22.09 and 38.29 Mb region. Although, this region is not very narrow, some of the genes falling in this region can be utilized for validation of QTLs in future. One differentially methylated region was found to be colocalized within the QTL intervals determined in Chr2 which indicates their potential role in epigenetic modifications in improving stress tolerance in rice.

PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data

BackgroundBulked segregant analysis (BSA), coupled with next-generation sequencing, allows the rapid identification of both qualitative and quantitative trait loci (QTL), and this technique is referred to as BSA-Seq here. The current SNP index method and G-statistic method for BSA-Seq data analysis require relatively high sequencing coverage to detect significant single nucleotide polymorphism (SNP)-trait associations, which leads to high sequencing cost.ResultsWe developed a simple and effective algorithm for BSA-Seq data analysis and implemented it in Python; the program was named PyBSASeq. Using PyBSASeq, the significant SNPs (sSNPs), SNPs likely associated with the trait, were identified via Fisher’s exact test, and then the ratio of the sSNPs to total SNPs in a chromosomal interval was used to detect the genomic regions that condition the trait of interest. The results obtained this way are similar to those generated via the current methods, but with more than five times higher sensitivity. This approach was termed the significant SNP method here.ConclusionsThe significant SNP method allows the detection of SNP-trait associations at much lower sequencing coverage than the current methods, leading to ~ 80% lower sequencing cost and making BSA-Seq more accessible to the research community and more applicable to the species with a large genome.

Genetic analysis of plant height and its components for wheat (<italic>Triticum aestivum </italic>L.) cultivars Ningmai 9 and Yangmai 158

<p indent=0mm>Ningmai 9 and Yangmai 158 are the main wheat cultivars and core parents in the middle and lower reaches of the Yangtze River in China. In the past three years, 80% of the released varieties in the middle and lower reaches of the Yangtze River had the background of Ningmai 9 or Yangmai 158. To make better use of these two parents, the genetic mechanism of their traits need to be further clarified. A high-density genetic map was constructed by Illumina 90k chip using 282 recombinant inbred lines (RILs) from the cross between Ningmai 9 and Yangmai 158. In this study, the traits including plant height, internode length, and spike length were determined in three consecutive growing seasons, and 14 stable QTLs were obtained by QTL mapping. By further position alignment, we focused on six chromosome intervals, which preliminarily revealed the genetic regulatory mechanism of the internode on plant height. KASP markers suitable for high-throughput analysis were developed based on the low-homology markers in the six chromosome intervals, and they were further validated in 101 wheat accessions. The polymerization of <italic>Qph-2D </italic>and <italic>Qph-5A.1</italic> had high selection efficiency which might be decreased if further intruding <italic>Q2A</italic>. It suggests that the selection of<italic> Q2A </italic>and<italic> Q5A</italic> should mainly focus on the alleles reducing plant height, and <italic>Qd1-5D </italic>could be used in marker-assisted selection for internode length below spike (D1). The results in this study may provide assistance for wheat height genetic improvement in the middle and lower reaches of the Yangtze River.

Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31.

We report a genomic and phenotypic delineation for two chromosome regions with candidate genes for syndromic intellectual disability at 12q12 and Xp22.31, segregating independently in one family with four affected members. Fine mapping of three affected members, along with six unreported small informative CNVs, narrowed down the candidate chromosomal interval to one gene LRRK2 at 12q12. Expression studies revealed high levels of LRRK2 transcripts in the whole human brain, cerebral cortex and hippocampus. RT-qPCR assays revealed that LRRK2 transcripts were dramatically reduced in our microdeletion patient DGDP289A compared to his healthy grandfather with no deletion. The decreased expression of LRRK2 may affect protein–protein interactions between LRRK2 and its binding partners, of which eight have previously been linked to intellectual disability. These findings corroborate with a role for LRRK2 in cognitive development, and, thus, we propose that intellectual disability and autism, displayed in the 12q12 microdeletions, are likely caused by LRRK2. Using another affected member, DGDP289B, with a microdeletion at Xp22.31, in this family, we performed the genomic and clinical delineation with six published and nine unreported cases. We propose HDHD1 and PNPLA4 for X-linked intellectual disability in this region, since their high transcript levels in the human brain substantiate their role in intellectual functioning.

Flag leaf size and posture of bread wheat: genetic dissection, QTL validation and their relationships with yield-related traits.

Major and environmentally stable QTL for flag leaf-related traits in wheat were identified and validated across ten environments using six populations with different genetic backgrounds. Flag leaf size and posture are two important factors of "ideotype" in wheat. Despite numerous studies on genetic analysis of flag leaf size including flag leaf length (FLL), width (FLW), area (FLA) and the ratio of length/width (FLR), few have focused on flag leaf posture including flag leaf angle (FLANG), opening angle (FLOA) and bend angle (FLBA). Further, the numbers of major, environmentally stable and verified genetic loci for flag leaf-related traits are limited. In this study, QTL for FLL, FLW, FLA, FLR, FLANG, FLOA and FLBA were identified based on a recombinant inbred line population together with values from up to ten different environments. Totally, eight major and stably expressed QTL were identified. Three co-located chromosomal intervals for seven major QTL were identified. The five major QTL QFll.sicau-5B.3 and QFll.sicau-2D.3 for FLL, QFlr.sicau-5B for FLR, QFlw.sicau-2D for FLW and QFla.sicau-2D for FLA were successfully validated by the tightly linked Kompetitive Allele Specific PCR (KASP) markers in the other five populations with different genetic backgrounds. A few genes related to leaf growth and development in intervals for these major QTL were predicated. Significant relationships between flag leaf- and yield-related traits were evidenced by analyses of Pearson correlations, conditional QTL and genetic mapping. Taken together, these results provide valuable information for understanding flag leaf size and posture of "ideotype" as well as fine mapping and breeding utilization of promising loci in bread wheat.

Genetic mapping of angular leaf spot resistance to Pseudomonas syringae pv. lachrymans in a Cucumis hystrix introgression line of cucumber

Angular leaf spot (ALS), caused by Pseudomonas syringae pv. lachrymans, is a common and devastating bacterial disease of cucumber worldwide. However, to the best of our knowledge, the report on genetic mapping of ALS resistance in cucumber is relatively few. In this study, IL52, a Cucumis hystrix introgression line of cucumber, was identified to be resistant to ALS. To investigate the inheritance and genomic location of the ALS resistance gene, IL52 was crossed with a susceptible parent changchunmici (CCMC) to develop F1 plant and 155 F6 recombinant inbred lines (RILs). The F1 plant was susceptible to ALS. The segregation ratio of ALS disease resistance in 155 RILs was 80:75 resistance/susceptibility, fitting to 1:1. The results indicated that a single recessive locus psl-1 was responsible for conferring resistance to ALS in IL52. Further, psl-1 was mapped into the 3,118,855–3,951,558 bp interval of chromosome 1 by combining molecular mapping with bulked segregant analysis and next-generation sequencing (BSA-seq). The marker ALS-InDel was found to be closely linked with psl-1 through the genetic linkage analysis in the 18 resistant RILs, 18 susceptible RILs and 19 susceptible cucumber cultivars. This study on genetic mapping of ALS resistance gene in a Cucumis hystrix introgression line of cucumber will be helpful for fine mapping and marker-assisted selection of ALS resistance gene.

Identification and fine mapping of qGN1c, a QTL for grain number per panicle, in rice (Oryza sativa)

Grain number per panicle (GN) is one of the most important determinants of grain yield potential in rice. However, the underlying genetic and molecular mechanisms that regulate GN remain largely unknown. In this study, quantitative trait loci (QTLs) for grain yield–related traits were detected using a set of chromosomal segment substitution lines (CSSLs) that were generated from a cross between the indica cultivar 9311 as the trait donor, and the japonica cultivar ‘Nipponbare’ as the recipient. In total, 25 QTLs for panicle-related traits, including GN, panicle length, primary branch number, and secondary branch number, were identified on eight chromosomes. Among the QTLs, qGN1c for GN was found to be located near Gn1a, a previously reported major QTL for GN on chromosome 1. Fine mapping placed qGN1c within a region of ~ 379 kb in a chromosomal interval flanking Gn1a, indicating that qGN1c is an uncloned gene. Evaluation of agronomic traits in a near isogenic line (NIL-qGN1c9311) suggested that qGN1c does not have additional impacts on agronomic traits except GN and thousand grain weight. More importantly, the grain yields per plant for the NIL-qGN1c9311 were significantly increased by 13.34% and 14.46% in two planting locations. Therefore, we conclude that the identification of qGN1c provides a useful genetic tool for the improvement of grain yield in rice breeding, and our findings will be helpful in cloning qGN1c.

Precision Phenotyping Reveals Novel Loci for Quantitative Resistance to Septoria Tritici Blotch.

Accurate, high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant breeding. We developed an automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. 335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform the GWAS. We identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four independent resistance traits. Sixteen of the intervals overlapped with known STB resistance intervals, suggesting that our phenotyping approach can identify simultaneously (i.e., in a single experiment) many previously defined STB resistance intervals. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance, perhaps representing resistance to pathogen strains that had not been tested in earlier experiments. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes. Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance.

Exploring and exploiting the genetic variation of Fusarium head blight resistance for genomic-assisted breeding in the elite durum wheat gene pool

Key messageGenomic selection had a higher selection response for FHB resistance than phenotypic selection, while association mapping identified major QTL on chromosome 3B unaffected by plant height and flowering date.Fusarium head blight (FHB) is one of the most destructive diseases of durum wheat. Hence, minimizing losses in yield, quality and avoiding contamination with mycotoxins are of pivotal importance, as durum wheat is mostly used for human consumption. While growing resistant varieties is the most promising approach for controlling this fungal disease, FHB resistance breeding in durum wheat is hampered by the limited variation in the elite gene pool and difficulties in efficiently combining the numerous small-effect resistance quantitative trait loci (QTL) in the same line. We evaluated an international collection of 228 genotyped durum wheat cultivars for FHB resistance over 3 years to investigate the genetic architecture and potential of genomic-assisted breeding for FHB resistance in durum wheat. Plant height was strongly positively correlated with FHB resistance and led to co-localization of plant height and resistance QTL. Nevertheless, a major QTL on chromosome 3B independent of plant height was identified in the same chromosomal interval as reported for the prominent hexaploid resistance QTL Fhb1, though haplotype analysis highlighted the distinctiveness of both QTL. Comparison between phenotypic and genomic selection for FHB resistance revealed a superior prediction ability of the former. However, simulated selection experiments resulted in higher selection responses when using genomic breeding values for early generation selection. An earlier identification of the most promising lines and crossing parents was feasible with a genomic selection index, which suggested a much faster short-term population improvement than previously possible in durum wheat, complementing long-term strategies with exotic resistance donors.

Semiautomated Feature Extraction from RGB Images for Sorghum Panicle Architecture GWAS

Because structural variation in the inflorescence architecture of cereal crops can influence yield, it is of interest to identify the genes responsible for this variation. However, the manual collection of inflorescence phenotypes can be time consuming for the large populations needed to conduct genome-wide association studies (GWAS) and is difficult for multidimensional traits such as volume. A semiautomated phenotyping pipeline, TIM (Toolkit for Inflorescence Measurement), was developed and used to extract unidimensional and multidimensional features from images of 1,064 sorghum (Sorghum bicolor) panicles from 272 genotypes comprising a subset of the Sorghum Association Panel. GWAS detected 35 unique single-nucleotide polymorphisms associated with variation in inflorescence architecture. The accuracy of the TIM pipeline is supported by the fact that several of these trait-associated single-nucleotide polymorphisms (TASs) are located within chromosomal regions associated with similar traits in previously published quantitative trait locus and GWAS analyses of sorghum. Additionally, sorghum homologs of maize (Zea mays) and rice (Oryza sativa) genes known to affect inflorescence architecture are enriched in the vicinities of TASs. Finally, our TASs are enriched within genomic regions that exhibit high levels of divergence between converted tropical lines and cultivars, consistent with the hypothesis that these chromosomal intervals were targets of selection during modern breeding.

A strategy for identifying markers linked with stem rust resistance in wheat harbouring an alien chromosome introgression from a non-sequenced genome.

A set of molecular markers was developed for Sr26 from comparative genomic analysis. The comparative genomic approach also enabled the identification of a previously uncharacterised wheat chromosome that carried Sr26. Stem rust of wheat, a biotic stress caused by a fungal pathogen, continues to pose significant threats to wheat production. Considerable effort has been directed at surveillance and breeding approaches to minimize the impact of the widely virulent race of the stem rust pathogen (Puccinia graminis f. sp. tritici, Pgt) commonly known as Ug99 (TTKSK) and other races in its lineage. The stem rust resistance gene Sr26, derived from Thinopyrum ponticum, is an excellent example of the successful utilization of a gene from a wild relative of a crop plant and remains one of the few durable sources of resistance currently effective against all known field isolates of Pgt. We explored comparative genomic analysis of the nucleotide binding leucine rich repeat (NLR) genes of the diploid D genome and bread wheat genomes to target the Sr26 region from the non-sequenced Th. ponticum genome. A chromosomal interval harboring NLR genes in the distal end of homoeologous group 6 chromosomes was used to demarcate the Sr26 locus. A set of closely linked PCR-based molecular markers was developed for Sr26. Furthermore, the comparative analysis approach enabled the unambiguous identification of a previously uncharacterised wheat chromosome that carried Sr26 in an introgressed Th. ponticum segment and was validated by fluorescent and genomic in situ hybridisation (FISH/GISH) experiments. The genetic information generated from the target interval based on this study will benefit future related studies on group 6 chromosomes of wheat, including 6Dt from Aegilops tauschii, and chromosome 6Ae#1 from Th. ponticum.

Mapping and Validation of Quantitative Trait Loci for Root Architectural Traits in Rice (&lt;i&gt;Oryza sativa&lt;/i&gt;) under Non-Stress and Salinity Stress Conditions

Root architectural traits are governed by many genes exhibiting polygenic inheritance. The dissection of the genetic basis of root traits could be achieved by mapping of quantitative trait loci (QTLs) using molecular markers. The present study was conducted aiming at identifying root QTLs in rice using a recombinant inbred line (RIL) population derived from At354 and Bg352. At354 has less extensive, thin root structure and Bg352 has apparently large extensive, dense root structure. Ninety one RILs were phenotypically assessed for root traits namely, root volume (RV), top root girth (TRG), root dry weight (RDW) and root length (RL) under hydroponics. Frequency distributions of these traits indicated broad spectrum of genetic variability in the RIL population. Quantitative Trait Loci (QTLs) were mapped using Single Nucleotide Polymorphism (SNP) markers investigated from a previous study corresponding to same RILs. Results revealed eight QTLs associated with TRG and RDW explaining phenotypic variation ranging from 8.3% to 14.8% under non-stress hydroponics. Identified root QTLs were located within the narrow flanking SNP marker intervals of chromosome 2, 4, 5, 7, 8 and 10. Of them, six root QTLs were co-localized exactly within the same flanking regions of previously identified root QTLs under salinity stress, indicating their contribution under both stress and non-stress conditions. The same donor alleles have contributed in both set of QTLs and these results validated and confirmed the fidelity of the QTLs detected on TRG and RDW. Moreover, this study found a closely associated, user friendly, simple sequence repeat marker, RM24894 to the QTL qNTRG10 and qNRDW10 which could facilitate marker assisted breeding.

Mapping of a dominant rust resistance gene revealed two R genes around the major Rust_QTL in cultivated peanut (Arachis hypogaea L.)

A consensus rust QTL was identified within a 1.25 cM map interval of A03 chromosome in cultivated peanut. This map interval contains a TIR-NB-LRR R gene and four pathogenesis-related genes. Disease resistance in plants is manifested due to the specific interaction between the R gene product and its cognate avirulence gene product (AVR) in the pathogen. Puccinia arachidis Speg. causes rust disease and inflicts economic damages to peanut. Till now, no experimental evidence is known for the action of R gene in peanut for rust resistance. A fine mapping approach towards the development of closely linked markers for rust resistance gene was undertaken in this study. Phenotyping of an RIL population at five environments for field rust score and subsequent QTL analysis has identified a 1.25cM map interval that harbored a consensus major Rust_QTL in A03 chromosome. This Rust_QTL is flanked by two SSR markers: FRS72 and SSR_GO340445. Both the markers clearly identified strong association of the mapped region with rust reaction in both resistant and susceptible genotypes from a collection of 95 cultivated peanut germplasm. This 1.25cM map interval contained 331.7kb in the physical map of A. duranensis and had a TIR-NB-LRR category R gene (Aradu.Z87JB) and four glucan endo-1,3 β glucosidase genes (Aradu.RKA6M, Aradu.T44NR, Aradu.IWV86 and Aradu.VG51Q). Another resistance gene analog was also found in the vicinity of mapped Rust_QTL. The sequence between SSR markers, FRS72 and FRS49, contains an LRR-PK (Aradu.JG217) which is equivalent to RHG4 in soybean. Probably, the protein kinase domain in AhRHG4 acts as an integrated decoy for the cognate AVR from Puccinia arachidis and helps the TIR-NB-LRR R-protein to initiate a controlled program cell death in resistant peanut plants.

Ligand-activated BMP signaling inhibits cell differentiation and death to promote melanoma.

Oncogenomic studies indicate that copy number variation (CNV) alters genes involved in tumor progression; however, identification of specific driver genes affected by CNV has been difficult, as these rearrangements are often contained in large chromosomal intervals among several bystander genes. Here, we addressed this problem and identified a CNV-targeted oncogene by performing comparative oncogenomics of human and zebrafish melanomas. We determined that the gene encoding growth differentiation factor 6 (GDF6), which is the ligand for the BMP family, is recurrently amplified and transcriptionally upregulated in melanoma. GDF6-induced BMP signaling maintained a trunk neural crest gene signature in melanomas. Additionally, GDF6 repressed the melanocyte differentiation gene MITF and the proapoptotic factor SOX9, thereby preventing differentiation, inhibiting cell death, and promoting tumor growth. GDF6 was specifically expressed in melanomas but not melanocytes. Moreover, GDF6 expression levels in melanomas were inversely correlated with patient survival. Our study has identified a fundamental role for GDF6 and BMP signaling in governing an embryonic cell gene signature to promote melanoma progression, thus providing potential opportunities for targeted therapy to treat GDF6-positive cancers.

Atypical autism in a boy with double duplication of 22q11.2: implications of increasing dosage

Duplication of chromosome 22q11.2 (LCR A-D) has been reported at higher frequencies in clinical samples than the general population, but phenotypes vary widely. Triplication (4 copies) is rare, but studying the associated phenotype may provide insight into dosage-sensitivity of the genes in this chromosomal interval. We describe a proband with a triplication, specifically a “double duplication” (two copies per chromosome) of the 22q11.2 region, while his parents and two siblings each have a single duplication (3 copies). The proband had a heart malformation, dysmorphic features, and learning and socialization deficits, whereas the other family members did not. This family illustrates that while duplication of the 22q11.2 may not be sufficient to cause clinically significant neurodevelopmental or health-related phenotypes, triplication of the same region may result in a phenotype characterized by a mild neurodevelopmental disorder, facial dysmorphism, and possibly cardiac anomalies.

QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza Sativa cultivars HR1128 and 'Nipponbare'.

Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar ‘Nipponbare’ as the donor and recurrent parents, respectively. The four panicle traits, GN, PL, PBN, and SBN, were evaluated for QTL effects using the inclusive composite interval mapping (ICIM) method in populations over two years at two sites. Results showed that a total of twelve QTLs for GN, PL, PBN, and SBN were detected on chromosome 6. Based on marker loci physical positions, the QTLs were found to be tightly linked to three important chromosomal intervals described as RM7213 to RM19962, RM20000 to RM20210, and RM412 to RM20595. Three QTLs identified in this study, PL6-5, PBN6-1, and PBN6-2, were found to be novel compared with previous studies. A major QTL (PL6-5) for panicle length was detected in all four populations at two locations, and its position was narrowed down to a 1.3Mb region on chromosome 6. Near isogenic lines (NILs) carrying PL6-5 will be developed for fine mapping of the QTL, and our results will provide referable information for gene excavation of panicle components in rice.

Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton.

A fiber length QTL, qFL-chr1, was fine mapped to a 0.9cM interval of cotton chromosome 1. Two positional candidate genes showed positive correlation between gene expression level and fiber length. Prior analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum L. and G. barbadense L. revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, a single NIIL, R01-40-08, was used to develop a large population segregating for the target region. Twenty-two PCR-based polymorphic markers used to genotype 1672 BC4F2 plants identified 432 recombinants containing breakpoints in the target region. Substitution mapping using 141 informative recombinants narrowed the position of qFL-chr1 to a 1.0-cM interval between SSR markers MUSS084 and CIR018. To exclude possible effects of non-target introgressions on fiber length, different heterozygous BC4F3 plants introgressed between SSR markers NAU3384 and CGR5144 were selected to develop sub-NILs. The qFL-chr1 was further mapped at 0.9-cM interval between MUSS422 and CIR018 by comparisons of sub-NIL phenotype, and increased fiber length by ~1mm. The 2.38-Mb region between MUSS422 and CIR018 in G. barbadense contained 19 annotated genes. Expression levels of two of these genes, GOBAR07705 (encoding 1-aminocyclopropane-1-carboxylate synthase) and GOBAR25992 (encoding amino acid permease), were positively correlated with fiber length in a small F2 population, supporting these genes as candidates for qFL-chr1.

Fine mapping of a distal chromosome 4 QTL affecting growth and muscle mass in a chicken advanced intercross line

In our previous research, QTL analysis in an F2 cross between the inbred New Hampshire (NHI) and White Leghorn (WL77) lines revealed a growth QTL in the distal part of chromosome 4. To physically reduce the chromosomal interval and the number of potential candidate genes, we performed fine mapping using individuals of generations F10 , F11 and F12 in an advanced intercross line that had been established from the initial F2 mapping population. Using nine single nucleotide polymorphism (SNP) markers within the QTL region for an association analysis with several growth traits from hatch to 20weeks and body composition traits at 20weeks, we could reduce the confidence interval from 26.9 to 3.4Mb. Within the fine mapped region, markers rs14490774, rs314961352 and rs318175270 were in full linkage disequilibrium (D'=1.0) and showed the strongest effect on growth and muscle mass (LOD≥4.00). This reduced region contains 30 genes, compared to 292 genes in the original region. Chicken 60K and 600K SNP chips combined with DNA sequencing of the parental lines were used to call mutations in the reduced region. In the narrowed-down region, 489 sequence variants were detected between NHI and WL77. The most deleterious variants are a missense variant in ADGRA3 (SIFT=0.02) and a frameshift deletion in the functional unknown gene ENSGALG00000014401 in NHI chicken. In addition, five synonymous variants were discovered in genes PPARGC1A, ADGRA3, PACRGL, SLIT2 and FAM184B. In our study, the confidence interval and the number of potential genes could be reduced 8- and 10- fold respectively. Further research will focus on functional effects of mutant genes.