Displaying publications 1 - 20 of 84 in total

  1. Sohrabi M, Rafii MY, Hanafi MM, Siti Nor Akmar A, Latif MA
    ScientificWorldJournal, 2012;2012:416291.
    PMID: 22654604 DOI: 10.1100/2012/416291
    Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.
    Matched MeSH terms: Quantitative Trait Loci/genetics*
  2. Mohd Sanusi NSN, Rosli R, Chan KL, Halim MAA, Ting NC, Singh R, et al.
    Comput Biol Chem, 2023 Feb;102:107801.
    PMID: 36528019 DOI: 10.1016/j.compbiolchem.2022.107801
    A high-quality reference genome is an important resource that can help decipher the genetic basis of traits in combination with linkage or association analyses. The publicly available oil palm draft genome sequence of AVROS pisifera (EG5) accounts for 1.535 Gb of the 1.8 Gb oil palm genome. However, the assemblies are fragmented, and the earlier assembly only had 43% of the sequences placed on pseudo-chromosomes. By integrating a number of SNP and SSR-based genetic maps, a consensus map (AM_EG5.1), comprising of 828.243 Mb genomic scaffolds anchored to 16 pseudo-chromosomes, was generated. This accounted for 54% of the genome assembly, which is a significant improvement to the original assembly. The total length of N50 scaffolds anchored to the pseudo-chromosomes increased by ∼18% compared to the previous assembly. A total of 139 quantitative trait loci for agronomically important quantitative traits, sourced from literature, were successfully mapped on the new pseudo-chromosomes. The improved assembly could also be used as a reference to identify potential errors in placement of specific markers in the linkage groups of the genetic maps used to assemble the consensus map. The 3422 unique markers from five genetic maps, anchored to the pseudo-chromosomes of AM_EG5.1, are an important resource that can be used preferentially to either construct new maps or fill gaps in existing genetic maps. Synteny analysis further revealed that the AM_EG5.1 had high collinearity with the date palm genome cultivar 'Barhee BC4' and shared most of its segmental duplications. This improved chromosomal-level genome is a valuable resource for genetic research in oil palm.
    Matched MeSH terms: Quantitative Trait Loci*
  3. Shamsudin NA, Swamy BP, Ratnam W, Sta Cruz MT, Raman A, Kumar A
    BMC Genet, 2016;17:30.
    PMID: 26818269 DOI: 10.1186/s12863-016-0334-0
    Three drought yield QTLs, qDTY 2.2, qDTY 3.1, and qDTY 12.1 with consistent effect on grain yield under reproductive stage drought stress were pyramided through marker assisted breeding with the objective of improving the grain yield of the elite Malaysian rice cultivar MR219 under reproductive stage drought stress. Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selection were performed. BC1F3-derived lines with different combinations of qDTY 2.2 , qDTY 3.1, and qDTY 12.1 were evaluated under both reproductive stage drought stress and non-stress during the dry seasons of 2013 and 2014 at IRRI.
    Matched MeSH terms: Quantitative Trait Loci
  4. Nevame AYM, Emon RM, Malek MA, Hasan MM, Alam MA, Muharam FM, et al.
    Biomed Res Int, 2018;2018:1653721.
    PMID: 30065932 DOI: 10.1155/2018/1653721
    Occurrence of chalkiness in rice is attributed to genetic and environmental factors, especially high temperature (HT). The HT induces heat stress, which in turn compromises many grain qualities, especially transparency. Chalkiness in rice is commonly studied together with other quality traits such as amylose content, gel consistency, and protein storage. In addition to the fundamental QTLs, some other QTLs have been identified which accelerate chalkiness occurrence under HT condition. In this review, some of the relatively stable chalkiness, amylose content, and gel consistency related QTLs have been presented well. Genetically, HT effect on chalkiness is explained by the location of certain chalkiness gene in the vicinity of high-temperature-responsive genes. With regard to stable QTL distribution and availability of potential material resources, there is still feasibility to find out novel stable QTLs related to chalkiness under HT condition. A better understanding of those achievements is essential to develop new rice varieties with a reduced chalky grain percentage. Therefore, we propose the pyramiding of relatively stable and nonallelic QTLs controlling low chalkiness endosperm into adaptable rice varieties as pragmatic approach to mitigate HT effect.
    Matched MeSH terms: Quantitative Trait Loci
  5. Barría A, Trịnh TQ, Mahmuddin M, Peñaloza C, Papadopoulou A, Gervais O, et al.
    Heredity (Edinb), 2021 Sep;127(3):334-343.
    PMID: 34262170 DOI: 10.1038/s41437-021-00447-4
    Enhancing host resistance to infectious disease has received increasing attention in recent years as a major goal of farm animal breeding programs. Combining field data with genomic tools can provide opportunities to understand the genetic architecture of disease resistance, leading to new opportunities for disease control. In the current study, a genome-wide association study was performed to assess resistance to the Tilapia lake virus (TiLV), one of the biggest threats affecting Nile tilapia (Oreochromis niloticus); a key aquaculture species globally. A pond outbreak of TiLV in a pedigreed population of the GIFT strain was observed, with 950 fish classified as either survivor or mortality, and genotyped using a 65 K SNP array. A significant QTL of large effect was identified on chromosome Oni22. The average mortality rate of tilapia homozygous for the resistance allele at the most significant SNP (P value = 4.51E-10) was 11%, compared to 43% for tilapia homozygous for the susceptibility allele. Several candidate genes related to host response to viral infection were identified within this QTL, including lgals17, vps52, and trim29. These results provide a rare example of a major QTL affecting a trait of major importance to a farmed animal. Genetic markers from the QTL region have potential in marker-assisted selection to improve host resistance, providing a genetic solution to an infectious disease where few other control or mitigation options currently exist.
    Matched MeSH terms: Quantitative Trait Loci
  6. Bhassu S, Abd Rashid Z
    Genetika, 2009 Sep;45(9):1244-9.
    PMID: 19824545
    The population structure of Probarbus jullieni from Malaysia and Thailand stocks was based on seven microsatellite primers and truss network measurements. Truss morphometric measurements were made on Temoleh, Probarbus jullieni to demonstrate the degree of speciation that can be induced by both biotic and abiotic conditions and contribute to the definition of different stocks of Probarbus sp. At the momment no relevant information on stock definition has been produced recently concerning Probarbus spp., which is now in IUCN threatened red list. We also summarize the possible discriminant morphological characteristics that shows differentiation between Malaysia and Thailand stocks. We also compare the levels of morphology and genetic differences for Malaysian stocks throughout one year of sampling to determine whether sampling season and possible sexual dimorphism can be detected in this fishes. A total of 25 different alleles were found across the two populations by the seven microsatellites, of which 21 and 19 alleles were detected in Pahang, Malaysia and Thailand, respectively At the population level, the mean number of alleles of Pahang (3.4991) per locus was higher than that (3.1665) of Thailand. From both molecular and morphometric measurements showed that there were two distinct populations. However the differences between these two populations showed that they belong to the same species with least degree of separation
    Matched MeSH terms: Quantitative Trait Loci/genetics*
  7. Bhassu S, Bakar Y, Rashid ZA
    Genetika, 2008 Aug;44(8):1145-7.
    PMID: 18825966
    Seven single locus dinucleotide microsatellite markers were developed to characterize an economically important sport fish and food fish in Malaysia and in Southeast Asia. They were obtained by using a rapid method namely the 5' anchored PCR enrichment protocol. The specific primers were designed to flank the repeat sequences and these were subsequently used to characterize 120 unrelated fish from Malaysia and 30 fishes from Indonesia. The number of alleles per locus ranged from 2 (SYKVJ1-11) to 6 (SYKVJ1-4) while the levels of heterozygosity ranged from 0.0472 (SYKVJ1-11) to 0.7745 (SYKVJ1-2).
    Matched MeSH terms: Quantitative Trait Loci/genetics*
  8. Ahmed F, Rafii MY, Ismail MR, Juraimi AS, Rahim HA, Asfaliza R, et al.
    Biomed Res Int, 2013;2013:963525.
    PMID: 23484164 DOI: 10.1155/2013/963525
    Submergence or flood is one of the major harmful abiotic stresses in the low-lying countries and crop losses due to waterlogging are considerably high. Plant breeding techniques, conventional or genetic engineering, might be an effective and economic way of developing crops to grow successfully in waterlogged condition. Marker assisted selection (MAS) is a new and more effective approach which can identify genomic regions of crops under stress, which could not be done previously. The discovery of comprehensive molecular linkage maps enables us to do the pyramiding of desirable traits to improve in submergence tolerance through MAS. However, because of genetic and environmental interaction, too many genes encoding a trait, and using undesirable populations the mapping of QTL was hampered to ensure proper growth and yield under waterlogged conditions Steady advances in the field of genomics and proteomics over the years will be helpful to increase the breeding programs which will help to accomplish a significant progress in the field crop variety development and also improvement in near future. Waterlogging response of soybean and major cereal crops, as rice, wheat, barley, and maize and discovery of QTL related with tolerance of waterlogging, development of resistant variety, and, in addition, future prospects have also been discussed.
    Matched MeSH terms: Quantitative Trait Loci*
  9. Teh CK, Ong AL, Mayes S, Massawe F, Appleton DR
    Genes (Basel), 2020 07 21;11(7).
    PMID: 32708151 DOI: 10.3390/genes11070826
    Superior oil yield is always the top priority of the oil palm industry. Short trunk height (THT) and compactness traits have become increasingly important to improve harvesting efficiency since the industry started to suffer yield losses due to labor shortages. Breeding populations with low THT and short frond length (FL) are actually available, such as Dumpy AVROS pisifera (DAV) and Gunung Melayu dura (GM). However, multiple trait stacking still remains a challenge for oil palm breeding, which usually requires 12-20 years to complete a breeding cycle. In this study, yield and height increment in the GM × GM (GM-3341) and the GM × DAV (GM-DAV-3461) crossing programs were evaluated and palms with good yield and smaller height increment were identified. In the GM-3341 family, non-linear THT growth between THT_2008 (seven years old) and THT_2014 (13 years old) was revealed by a moderate correlation, suggesting that inter-palm competition becomes increasingly important. In total, 19 quantitative trait loci (QTLs) for THT_2008 (8), oil per palm (O/P) (7) and FL (4) were localized on the GM-3341 linkage map, with an average mapping interval of 2.01 cM. Three major QTLs for THT_2008, O/P and FL are co-located on chromosome 11 and reflect the correlation of THT_2008 with O/P and FL. Multiple trait selection for high O/P and low THT (based on the cumulative effects of positive alleles per trait) identified one palm from 100 palms, but with a large starting population of 1000-1500 seedling per cross, this low frequency could be easily compensated for during breeding selection.
    Matched MeSH terms: Quantitative Trait Loci*
  10. Poh KB, Roslan ZM, Misnan R, Sinang SC
    J Genet, 2018 Sep;97(4):817-824.
    PMID: 30262693
    Msb069 primer pairs encompassed region is believed to be associated with a quantitative trait loci (QTL) of dorsal fin length in subgenus Poecilia. However, detailed investigation on Msb069 which originated from Xiphophorus on subgenus Poecilia remains unexplored. In this study, full sequence of Msb069 was characterized by sequencing bioinformatics analysis and gene expression. The sequence analysis of Msb069 primer pairs encompassed region on three species of Poecilia revealed higher number of microsatellite tandem repeats in Poecilia latipinna (ATG
    ) compared to P. sphenops (ATG
    ). There is no notable pattern of ATGtandem repeats discovered in the hybrids. The full sequence of Msb069 is 734 bp in length and showed a 233 bp conserved region between Xiphophorus and Poecilia. BLAST search performed on this sequence revealed no significant similarities. Nonquantitative RT-PCR exhibited the presence of Msb069 transcripts in three different tissues in subgenus Poecilia. Meanwhile, quantitative RTPCR expression on two different tissues showed relatively higher expression of Msb069 transcript in P. latipinna dorsal fin tissues in both male and female fishes, suggesting a repressive function of this transcript with respect to dorsal fin length. However the exact gene expression event of Msb069 is still unknown and requires further investigation.
    Matched MeSH terms: Quantitative Trait Loci/genetics
  11. Glubb DM, Thompson DJ, Aben KKH, Alsulimani A, Amant F, Annibali D, et al.
    Cancer Epidemiol Biomarkers Prev, 2021 Jan;30(1):217-228.
    PMID: 33144283 DOI: 10.1158/1055-9965.EPI-20-0739
    BACKGROUND: Accumulating evidence suggests a relationship between endometrial cancer and ovarian cancer. Independent genome-wide association studies (GWAS) for endometrial cancer and ovarian cancer have identified 16 and 27 risk regions, respectively, four of which overlap between the two cancers. We aimed to identify joint endometrial and ovarian cancer risk loci by performing a meta-analysis of GWAS summary statistics from these two cancers.

    METHODS: Using LDScore regression, we explored the genetic correlation between endometrial cancer and ovarian cancer. To identify loci associated with the risk of both cancers, we implemented a pipeline of statistical genetic analyses (i.e., inverse-variance meta-analysis, colocalization, and M-values) and performed analyses stratified by subtype. Candidate target genes were then prioritized using functional genomic data.

    RESULTS: Genetic correlation analysis revealed significant genetic correlation between the two cancers (rG = 0.43, P = 2.66 × 10-5). We found seven loci associated with risk for both cancers (P Bonferroni < 2.4 × 10-9). In addition, four novel subgenome-wide regions at 7p22.2, 7q22.1, 9p12, and 11q13.3 were identified (P < 5 × 10-7). Promoter-associated HiChIP chromatin loops from immortalized endometrium and ovarian cell lines and expression quantitative trait loci data highlighted candidate target genes for further investigation.

    CONCLUSIONS: Using cross-cancer GWAS meta-analysis, we have identified several joint endometrial and ovarian cancer risk loci and candidate target genes for future functional analysis.

    IMPACT: Our research highlights the shared genetic relationship between endometrial cancer and ovarian cancer. Further studies in larger sample sets are required to confirm our findings.

    Matched MeSH terms: Quantitative Trait Loci/genetics
  12. Cross-Disorder Group of the Psychiatric Genomics Consortium. Electronic address: plee0@mgh.harvard.edu, Cross-Disorder Group of the Psychiatric Genomics Consortium
    Cell, 2019 Dec 12;179(7):1469-1482.e11.
    PMID: 31835028 DOI: 10.1016/j.cell.2019.11.020
    Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci. However, the nature and mechanisms of these pleiotropic effects remain unclear. We performed analyses of 232,964 cases and 494,162 controls from genome-wide studies of anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, and Tourette syndrome. Genetic correlation analyses revealed a meaningful structure within the eight disorders, identifying three groups of inter-related disorders. Meta-analysis across these eight disorders detected 109 loci associated with at least two psychiatric disorders, including 23 loci with pleiotropic effects on four or more disorders and 11 loci with antagonistic effects on multiple disorders. The pleiotropic loci are located within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes. These findings have important implications for psychiatric nosology, drug development, and risk prediction.
    Matched MeSH terms: Quantitative Trait Loci*
  13. Ali MN, Yeasmin L, Gantait S, Goswami R, Chakraborty S
    Physiol Mol Biol Plants, 2014 Oct;20(4):411-23.
    PMID: 25320465 DOI: 10.1007/s12298-014-0250-6
    The present investigation was carried out to evaluate 33 rice landrace genotypes for assessment of their salt tolerance at seedling stage. Growth parameters like root length, shoot length and plant biomass were measured after 12 days of exposure to six different levels of saline solution (with electrical conductivity of 4, 6, 8, 10, 12 or 14 dS m (-1)). Genotypes showing significant interaction and differential response towards salinity were assessed at molecular level using 11 simple sequence repeats (SSR) markers, linked with salt tolerance quantitative trait loci. Shoot length, root length and plant biomass at seedling stage decreased with increasing salinity. However, relative salt tolerance in terms of these three parameters varied among genotypes. Out of the 11 SSR markers RM8094, RM336 and RM8046, the most competent descriptors to screen the salt tolerant genotypes with higher polymorphic information content coupled with higher marker index value, significantly distinguished the salt tolerant genotypes. Combining morphological and molecular assessment, four lanraces viz. Gheus, Ghunsi, Kuthiahara and Sholerpona were considered as true salt tolerant genotypes which may contribute in greater way in the development of salt tolerant genotypes in rice.
    Matched MeSH terms: Quantitative Trait Loci
  14. Mohd Ikmal A, Nurasyikin Z, Tuan Nur Aqlili Riana TA, Puteri Dinie Ellina Z, Wickneswari R, Noraziyah AAS
    Plants (Basel), 2019 Jun 24;8(6).
    PMID: 31238548 DOI: 10.3390/plants8060186
    Drought has been a major limiting factor for rice production. Drought yield QTLs (qDTYs; QTLs = quantitative trait loci) were pyramided into MRQ74 and MR219 to produce drought tolerant lines. In this study, new drought tolerant MRQ74 and MR219 pyramided lines (PLs) were evaluated under drought stress (RS) and non-stress (NS) conditions to evaluate the effects of different qDTYs combinations on morphological and agronomical traits. MRQ74 PLs having qDTY12.1 possessed the best root length (RL) under both RS and NS but the effect was only significant for MR219 PLs under RS. Some qDTYs combinations also found to have consistent effect on the same trait of both populations. PLs with only qDTY12.1 showed the highest grain yield (GY) under RS in both populations which means qDTY12.1 controlled RL and caused higher GY under drought condition. The interaction of major-effect qDTY12.1 with qDTY2.2 also shows significant effect on leaf rolling (LR) of both PL populations. These qDTYs proved to be beneficial in improving traits related to drought tolerance. Selected PLs with qDTY12.1 combinations also found to have better RL and root weight (RW) under RS. Improvement of morphological and agronomical traits led to higher GY of PLs. Therefore, qDTY12.1 either is present singly or in combination with other qDTYs was the best qDTY due to its consistent effect on morphological and agronomical traits and GY across populations under RS and NS.
    Matched MeSH terms: Quantitative Trait Loci
  15. Jahan N, Javed MA, Khan A, Manan FA, Tabassum B
    Ecotoxicology, 2021 Jul;30(5):794-805.
    PMID: 33871748 DOI: 10.1007/s10646-021-02413-6
    Aluminum (Al3+) toxicity is one of the factors limiting crop production in acidic soils. Identifying quantitative trait loci (QTLs)/genes for tolerance to Al3+ toxicity at seed germination can aid the development of new tolerant cultivars. The segregating population derived from Pak Basmati (Indica) × Pokkali (Indica) was used for mapping QTLs linked with tolerance to Al3+ toxicity ranging from 0 to 20 mM at pH 4 ± 0.2 at germination. The favorable alleles for all new QTLs were analyzed based on germination traits, i.e., final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean germination time (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC), and growth traits, such as root length (RL), shoot length (SL), total dry biomass (TDB) and germination vigor index (GVI). The phenotypic evolution showed transgressive variations. For genome-wide mapping, 90 polymorphic SSRs with 4 gene-specific markers and Win QTL Cart were used for QTL analysis. In all, 35 QTLs for germination and 11 QTLs for seedling growth were detected in distinct chromosomal regions by composite interval mapping (CIM), and multiple interval mapping (MIM) confirmed the pleiotropy at region RM128 on chromosome 1. Based on our genetic mapping studies, the genes/QTLs underlying tolerance to Al3+ toxicity could differ for both the germination and seedling stages in segregated populations. The QTLs identified in this study could be a source of new alleles for improving tolerance to Al3+ toxicity in rice.
    Matched MeSH terms: Quantitative Trait Loci
  16. Mohd Ikmal A, Noraziyah AAS, Wickneswari R
    Plants (Basel), 2021 Jan 24;10(2).
    PMID: 33498963 DOI: 10.3390/plants10020225
    Drought and submergence have been the major constraint in rice production. The present study was conducted to develop high-yielding rice lines with tolerance to drought and submergence by introgressing Sub1 into a rice line with drought yield QTL (qDTY; QTL = quantitative trait loci) viz. qDTY3.1 and qDTY12.1 using marker-assisted breeding. We report here the effect of different combinations of Sub1 and qDTY on morpho-physiological, agronomical traits and yield under reproductive stage drought stress (RS) and non-stress (NS) conditions. Lines with outstanding performance in RS and NS trials were also evaluated in vegetative stage submergence stress (VS) trial to assess the tolerance level. The QTL class analysis revealed Sub1 + qDTY3.1 as the best QTL combination affecting the measured traits in RS trial followed by Sub1 + qDTY12.1. The effects of single Sub1, qDTY3.1 and qDTY12.1 were not as superior as when the QTLs are combined, suggesting the positive interaction of Sub1 and qDTY. Best performing lines selected from the RS and NS trials recorded yield advantage up to 4453.69 kg ha-1 and 6954 kg ha-1 over the parents, respectively. The lines were also found having great tolerance to submergence ranging from 80% to 100%, contributed by a lower percentage of shoot elongation and reduction of chlorophyll content after 14 days of VS. These lines could provide yield sustainability to farmers in regions impacted with drought and submergence while serving as important genetic materials for future breeding programs.
    Matched MeSH terms: Quantitative Trait Loci
  17. Catolos M, Sandhu N, Dixit S, Shamsudin NAA, Naredo MEB, McNally KL, et al.
    Front Plant Sci, 2017;8:1763.
    PMID: 29085383 DOI: 10.3389/fpls.2017.01763
    Drought is the major abiotic stress to rice grain yield under unpredictable changing climatic scenarios. The widely grown, high yielding but drought susceptible rice varieties need to be improved by unraveling the genomic regions controlling traits enhancing drought tolerance. The present study was conducted with the aim to identify quantitative trait loci (QTLs) for grain yield and root development traits under irrigated non-stress and reproductive-stage drought stress in both lowland and upland situations. A mapping population consisting of 480 lines derived from a cross between Dular (drought-tolerant) and IR64-21 (drought susceptible) was used. QTL analysis revealed three major consistent-effect QTLs for grain yield (qDTY1.1, qDTY1.3 , and qDTY8.1 ) under non-stress and reproductive-stage drought stress conditions, and 2 QTLs for root traits (qRT9.1 for root-growth angle and qRT5.1 for multiple root traits, i.e., seedling-stage root length, root dry weight and crown root number). The genetic locus qDTY1.1 was identified as hotspot for grain yield and yield-related agronomic and root traits. The study identified significant positive correlations among numbers of crown roots and mesocotyl length at the seedling stage and root length and root dry weight at depth at later stages with grain yield and yield-related traits. Under reproductive stage drought stress, the grain yield advantage of the lines with QTLs ranged from 24.1 to 108.9% under upland and 3.0-22.7% under lowland conditions over the lines without QTLs. The lines with QTL combinations qDTY1.3 +qDTY8.1 showed the highest mean grain yield advantage followed by lines having qDTY1.1 +qDTY8.1 and qDTY1.1 +qDTY8.1 +qDTY1.3 , across upland/lowland reproductive-stage drought stress. The identified QTLs for root traits, mesocotyl length, grain yield and yield-related traits can be immediately deployed in marker-assisted breeding to develop drought tolerant high yielding rice varieties.
    Matched MeSH terms: Quantitative Trait Loci
  18. Jiang DL, Gu XH, Li BJ, Zhu ZX, Qin H, Meng ZN, et al.
    Mar Biotechnol (NY), 2019 Apr;21(2):250-261.
    PMID: 30737627 DOI: 10.1007/s10126-019-09877-y
    Understanding the genetic mechanism of osmoregulation is important for the improvement of salt tolerance in tilapia. In our previous study, we have identified a major quantitative trait locus (QTL) region located at 23.0 Mb of chrLG18 in a Nile tilapia line by QTL-seq. However, the conservation of these QTLs in other tilapia populations or species is not clear. In this study, we successfully investigated the QTLs associated with salt tolerance in a mass cross population from the GIFT line of Nile tilapia (Oreochromis niloticus) using a ddRAD-seq-based genome-wide association study (GWAS) and in a full-sib family from the Malaysia red tilapia strain (Oreochromis spp) using QTL-seq. Our study confirmed the major QTL interval that is located at nearly 23.0 Mb of chrLG18 in Nile tilapia and revealed a long QTL cluster across chrLG18 controlling for the salt-tolerant trait in both red tilapia and Nile tilapia. This is the first GWAS analysis on salt tolerance in tilapia. Our finding provides important insights into the genetic architecture of salinity tolerance in tilapia and supplies a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the underlying genes for salt tolerance in tilapia.
    Matched MeSH terms: Quantitative Trait Loci
  19. Yeo FKS, Bouchon R, Kuijken R, Loriaux A, Boyd C, Niks RE, et al.
    PMID: 28356783 DOI: 10.1007/s11032-017-0624-x
    Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P. hordei will allow elucidation of the molecular basis of this type of plant defence. A map-based cloning approach requires to fine-map the QTL in a narrow genetic window. In this study, Rphq11 and rphq16 were fine-mapped using an approach aiming at speeding up the development of plant material and simplifying its evaluation. The plant materials for fine-mapping were identified from early plant materials developed to produce QTL-NILs. The material was first selected to carry the targeted QTL in heterozygous condition and susceptibility alleles at other resistance QTLs in homozygous condition. This strategy took four to five generations to obtain fixed QTL recombinants (i.e., homozygous resistant at the Rphq11 or rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). In less than 2 years, Rphq11 was fine-mapped into a 0.2-cM genetic interval and a 1.4-cM genetic interval for rphq16. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase. Thus far, no candidate gene was identified for rphq16.
    Matched MeSH terms: Quantitative Trait Loci
  20. Ngu MS, Thomson MJ, Bhuiyan MA, Ho C, Wickneswari R
    Genet. Mol. Res., 2014;13(4):9477-88.
    PMID: 25501158 DOI: 10.4238/2014.November.11.13
    Grain weight is a major component of rice grain yield and is controlled by quantitative trait loci. Previously, a rice grain weight quantitative trait locus (qGW6) was detected near marker RM587 on chromosome 6 in a backcross population (BC2F2) derived from a cross between Oryza rufipogon IRGC105491 and O. sativa cv. MR219. Using a BC2F5 population, qGW6 was validated and mapped to a region of 4.8 cM (1.2 Mb) in the interval between RM508 and RM588. Fine mapping using a series of BC4F3 near isogenic lines further narrowed the interval containing qGW6 to 88 kb between markers RM19268 and RM19271.1. According to the Duncan multiple range test, 8 BC4F4 near isogenic lines had significantly higher 100-grain weight (4.8 to 7.5% over MR219) than their recurrent parent, MR219 (P < 0.05). According to the rice genome automated annotation database, there are 20 predicted genes in the 88-kb target region, and 9 of them have known functions. Among the genes with known functions in the target region, in silico gene expression analysis showed that 9 were differentially expressed during the seed development stage(s) from gene expression series GSE6893; however, only 3 of them have known functions. These candidates provide targets for further characterization of qGW6, which will assist in understanding the genetic control of grain weight in rice.
    Matched MeSH terms: Quantitative Trait Loci/genetics*
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