scholarly journals Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1369
Author(s):  
Dan-Dan Zhao ◽  
Ju-Hyeong Son ◽  
Muhammad Farooq ◽  
Kyung-Min Kim
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Middle Part ◽  
Internode Length ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Doubled Haploid Population ◽  
Lodging Resistance ◽  
Cytochrome P450 Family ◽  
Uppermost Internode

Internode length and stem diameter are the primary traits affecting the lodging resistance of rice. Traits related to the length of the panicle (LP), uppermost internode (LUI), second internode (LSI), third internode (LTI), fourth internode (LFI), lowest internode (LLI) as well as stem diameter at the uppermost internode (SDUI), second internode (SDSI), third internode (SDTI), fourth internode (SDFI), and lowest internode (SDLI) in 120 Cheongcheong/Nagdong doubled haploid population were investigated using a quantitative trait locus (QTL) analysis. Thirty-four QTL regions affected LP and the length of each internode. Twenty-six QTL regions were associated with the stem diameter of each internode. RM12285-RM212 on chromosome 1 contained 10 QTLs related to the internode length, which have overlapped for over 2 years. Twenty-three candidate genes were screened using mark interval. Among the candidate genes, Os01g0803900, named OsCYPq1, which is in the Cytochrome P450 family, might be involved in gibberellins (GA) synthesis. GA is an essential plant growth regulator that affects plant height. OsCYPq1 catalyzes oxidation steps in the middle part of the GA pathway. OsCYPq1 is expected to provide valuable information to improve the marker assessment for target traits and QTL gene cloning in rice.

scholarly journals Deciphering the genetics basis of lodging resistance in wild rice O. longistaminata

2019 ◽  
Author(s):  
Weixiong Long ◽  
Dong Dan ◽  
Zhengqing Yuan ◽  
Yunping Chen ◽  
Jie Jin ◽  
...  
Keyword(s):  
Wild Rice ◽  
High Throughput Sequencing ◽  
Breaking Strength ◽  
Chromosome 8 ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Stem Length ◽  
Cultivated Rice ◽  
Lodging Resistance ◽  
Major Qtl

Abstract The abuse of fertilizer results in tall rice plants that are susceptible to lodging and reduced plant yield. Hence, it is important to identify and utilize the QTLs/genes for lodging resistance breeding. O. longistaminata exhibited a strong stem and high biomass productively, which could be the candidate gene pool for cultivars lodging resistance improvement. However, most of previous studies have focused on cultivated rice and few reports on wild rice. Here, a set of 152 BC 2 F 20 lines derived from a cross between 93-11 and O. longistaminata were evaluated for lodging resistance. QTL mapping analysis combined with SNP marker derived from high-throughput sequencing identified 12 QTLs for stem diameter (SD), 11 QTLs for stem length (SL) and 3 QTLs for breaking strength (BS). Of which, 14 QTLs were firstly identified from O. longistaminata. A major QTL, qLR1 which was delimited to a region about 80 Kb on chromosome 1, increased stem diameter, stem length and breaking strength. And another major QTL, qLR8 that was delimited in an interval about 100 Kb on chromosome 8, significantly enhanced the breaking strength. These results provide evidence that the O. longistaminata can be exploited to develop lodging resistant rice lines.

scholarly journals Screening for a Novel Gene, OsPSLSq6, Using QTL Analysis for Lodging Resistance in Rice

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 334
Author(s):  
Dan-Dan Zhao ◽  
Ju Hyeong Son ◽  
Gang-Seob Lee ◽  
Kyung-Min Kim
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Common Factor ◽  
Heading Date ◽  
Lignin Biosynthesis ◽  
Defense Responses ◽  
Resistant Variety ◽  
Chromosome 6 ◽  
Lodging Resistance ◽  
Lower Stem

Lodging is the most common factor that affects crop productivity, reducing yield, grain quality, and harvesting efficiency of rice and other cereal crops. The Cheongcheong (Indica)/Nagdong (Japonica) doubled haploid (CNDH) genetic map was used to develop a lodging-resistant variety. The major agricultural traits of rice related to lodging resistance, such as the pushing strength of the lower stem before the heading date (PSLSB) at reproductive growth period and pushing strength of the lower stem after the heading date (PSLSA) at full ripe period were investigated. A quantitative trait locus (QTL) analysis of PSLSA and PSLSB detected on RM439-RM20318 on chromosome 6 has overlap in three consecutive years. RM439-RM20318 on chromosome 6 contained 15 lodging resistance candidate genes. Among the candidate genes, Os06g0623200, named OsPSLSq6, which is similar to Cinnamoyl-CoA reductase, involved lignin biosynthesis in defense responses. Lignin is the main structural component of vascular plants’ secondary cell wall, which is not only related to plant growth and development but also to mechanical strength. OsPSLSq6 opens new possibilities to control lignin synthesis to improve lodging resistance. OsPSLSq6 can be used as a target gene for further studies to provide important information for the marker-assisted improvement of target traits and cloning genes underlying the QTL of interest.

QTL Analysis of Under-ear Internode Length Based on SSSL Population

2018 ◽  
Vol 44 (4) ◽  
pp. 522
Author(s):  
Hai-Ping GUO ◽  
Gao-Yang SUN ◽  
Xiao-Xiang ZHANG ◽  
Peng-Shuai YAN ◽  
Kun LIU ◽  
...  
Keyword(s):  
Qtl Analysis ◽  
Internode Length

scholarly journals Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jose Miguel Soriano ◽  
Pasqualina Colasuonno ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta
Keyword(s):  
Molecular Markers ◽  
Abiotic Stress ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Biotic Stress ◽  
Qtl Analysis ◽  
Complex Traits ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

scholarly journals Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 718
Author(s):  
Bingxin Meng ◽  
Tao Wang ◽  
Yi Luo ◽  
Deze Xu ◽  
Lanzhi Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Genome Wide Association ◽  
Lodging Resistance ◽  
Leaf Type ◽  
Stem Strength ◽  
Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

Improvement of lodging resistance with QTLs for stem diameter in rice (Oryza sativa L.)

2008 ◽  
Vol 117 (5) ◽  
pp. 749-757 ◽  
Author(s):  
Takayuki Kashiwagi ◽  
Eiji Togawa ◽  
Naoki Hirotsu ◽  
Ken Ishimaru
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Stem Diameter ◽  
Lodging Resistance

Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens

Genome ◽  
2020 ◽  
Vol 63 (3) ◽  
pp. 133-143 ◽  
Author(s):  
Jun Guo ◽  
Liang Qu ◽  
Tao-Cun Dou ◽  
Man-Man Shen ◽  
Yu-Ping Hu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Linear Mixed Model ◽  
Bone Size ◽  
Chromosome 1 ◽  
Meat Production ◽  
Phenotypic Variance ◽  
Femur Length ◽  
Genome Wide ◽  
Length And Area ◽  
Tibia Length

Bone size is an important trait for chickens because of its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12 ± 0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area, and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb harbored HTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.

Genetic Susceptibility to Therapy-Related Acute Murine Promyelocytic Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 14-14
Author(s):  
Ryan K. Funk ◽  
Taylor Maxwell ◽  
Masayo Izumi ◽  
Deepa Edwin ◽  
Friederike Kreisel ◽  
...  
Keyword(s):  
Median Survival ◽  
Qtl Analysis ◽  
Myeloid Leukemia ◽  
Single Copy ◽  
Promyelocytic Leukemia ◽  
Myelogenous Leukemia ◽  
Chromosome 1 ◽  
Mouse Strains ◽  
Spleen Weight ◽  
Trait Locus

Abstract Therapy-related acute myelogenous leukemia (t-AML) is an important late adverse effect of alkylator chemotherapy. Susceptibility to t-AML has a genetic component, yet the specific genes and genetic variations that influence susceptibility are poorly understood. Our lab previously identified mouse strains that are susceptible (SWR/J) or resistant (C57BL/6J and C3H/HeJ) to t-AML induced by the alkylator, ethyl-N-nitrosourea (ENU). To study the genetic basis of these differences, we performed an F2 intercross between susceptible and resistant strains. A single copy of the hCG-PML-RARa (PR) transgene was bred into each mouse. PR is an initiating factor for acute promyelocytic leukemia, but requires cooperating mutations for full leukemic transformation. This provides a platform to detect gene X transgene (PR) and gene X environment (ENU) interactions that promote leukemogenesis. F2 mice were treated (n=141) or untreated (n=141) with ENU and sacrificed and analyzed when moribund. We also analyzed untreated PR+ (n=24) mice from the resistant C57BL/6J X C3H/HeJ (B6C3F1) background. Untreated B6C3F1 PR+ mice developed lethal myeloid leukemia (characterized by splenomegaly > 0.25g, WBC > 30 K/uL, and increased immature myeloid precursors in PB, BM, and spleen) with an incidence of 12.5% and a latency of 234 days. By contrast, 79.4% of untreated PR+ F2 mice developed myeloid leukemia with a latency of 108 days and median survival of 238 days. The earlier onset and increased incidence of leukemia in F2 mice confirm that SWR/J alleles confer increased susceptibility to AML. ENU treatment further increased the leukemia incidence (90.4% vs. 79.4%, p<0.0001 by logrank) and shortened the median survival (168 vs. 238 days) of PR+ F2 mice. F2 mice were genotyped using 357 informative SNPs across the genome to facilitate quantitative trait locus (QTL) mapping. QTL analysis was performed using leukemia-free survival, spleen weight, and WBC as quantitative traits. Because extramedullary hematopoeisis and increased WBC are markers of poor prognosis in human AML, we reasoned that identification of modifier alleles for these traits might also have potential clinical relevance. QTL analysis revealed five peaks associated with survival, 5 with spleen weight, and 3 with WBC. The 1 LPR (likelihood probability ratio) confidence intervals for the QTL range in size from 10 to 50 Mbp. Each region contains between 100 and 750 genes. The most significant peak (LPR=3.94) is a survival QTL on chromosome 1 from 93.4 to 120.5 Mbp that retains significance at the genome wide level. The QTL effect is large in ENU-treated animals but not discernible in untreated animals. Both the additive effect (−0.51, SE=0.17) and the dominant effect (0.62, SE=0.20) are significant at p<0.05. Genes with potential connections to leukemogenesis within this region include a serpin cluster, genes involved in apoptosis (Bcl2, Bok, Pdcd1 Phlpp), and cell cycle genes (Sept2 and Clasp1). Ongoing studies are focused on candidate gene evaluation and fine-mapping the QTL regions to identify the QTL genes and their variants. Validation of these genes in therapy-related leukemogenesis should provide a better understanding of t-AML susceptibility and lead to strategies that moderate t-AML risk in susceptible individuals.

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