scholarly journals QTL Mapping And Candidate Gene Mining of Flag Leaf Size Traits In Japonica Rice Based On Linkage Mapping And Genome-Wide Association Study

2021 ◽  
Author(s):  
Wang Jiangxu ◽  
Wang Tao ◽  
Wang qi ◽  
Tang Xiaodong ◽  
Ren Yang ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Association Study ◽  
Leaf Development ◽  
Molecular Breeding ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Leaf Shape ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Flag Leaf Width

Abstract As one of the most important part of the ideal plant type of japonica rice, leaf shape affects the photosynthesis and carbohydrate accumulation directly. Mining and using new leaf shape related genes/QTLs can further enrich the theory of molecular breeding and accelerate the breeding process of japonica rice. In the present study, 2 RILs and a natural population with 295 japonica rice varieties were used to map QTLs for flag leaf length (FL), flag leaf width (FW) and flag leaf area (FLA) by linkage analysis and genome-wide association study (GWAS) through 2 years. A total of 64 QTLs were detected by 2 ways, and pleiotropic QTLs qFL2 (Chr2_33,332,579) and qFL10 (Chr10_10,107,835; Chr10_10,230,100) consisted of overlapping QTLs mapped by linkage analysis and GWAS through 2 years were identified. The candidate genes LOC_Os02g54254, LOC_Os02g54550, LOC_Os10g20160, LOC_Os10g20240, LOC_Os10g20260 were obtained, filtered by linkage disequilibrium (LD), and haplotype analysis. LOC_Os10g20160 (SD-RLK-45) showed outstanding characteristics in quantitative real-time PCR (qRT-PCR) analysis in leaf development period, belongs to S-domain receptor-like protein kinases gene and probably to be a main gene regulating flag leaf width of japonica rice. The results of this study provide valuable resources for mining the main genes/QTLs of japonica rice leaf development and molecular breeding of japonica rice ideal leaf shape.

Linkage Analysis and Genome-Wide Association Study of QTLs Controlling Stem-Breaking-Strength-Related Traits in Wheat

2017 ◽  
Vol 43 (4) ◽  
pp. 483 ◽  
Author(s):  
Kai LIU ◽  
Zhi-Ying DENG ◽  
Ying ZHANG ◽  
Fang-Fang WANG ◽  
Tong-Tong LIU ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Breaking Strength ◽  
Genome Wide Association ◽  
Genome Wide

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.

Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study

2018 ◽  
Vol 131 (5) ◽  
pp. 1073-1090 ◽  
Author(s):  
Kai Liu ◽  
Xiaoxiao Sun ◽  
Tangyuan Ning ◽  
Xixian Duan ◽  
Qiaoling Wang ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genetic Dissection ◽  
Genome Wide ◽  
A Genome ◽  
Panicle Traits

Genome-wide association study and linkage analysis on resistance to rice black-streaked dwarf virus disease

2019 ◽  
Vol 39 (5) ◽  
Author(s):  
Shizhuo Xiao ◽  
Baoxiang Wang ◽  
Yuqiang Liu ◽  
Tianhui Miao ◽  
Hongliang Zhang ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Virus Disease ◽  
Genome Wide Association ◽  
Dwarf Virus ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Reveals Genomic Region Associated with Mite-Recruitment Phenotypes in the Domesticated Grapevine (Vitis vinifera)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1013
Author(s):  
Erika R. LaPlante ◽  
Margaret B. Fleming ◽  
Zoë Migicovsky ◽  
Marjorie Gail Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Plant Traits ◽  
Leaf Shape ◽  
Common Garden ◽  
Genome Wide Association ◽  
Genetic Associations ◽  
Predacious Mites ◽  
Genome Wide ◽  
A Genome

Indirect defenses are plant phenotypes that reduce damage by attracting natural enemies of plant pests and pathogens to leaves. Despite their economic and ecological importance, few studies have investigated the genetic underpinnings of indirect defense phenotypes. Here, we present a genome-wide association study of five phenotypes previously determined to increase populations of beneficial (fungivorous and predacious) mites on grape leaves (genus Vitis): leaf bristles, leaf hairs, and the size, density, and depth of leaf domatia. Using a common garden genetic panel of 399 V. vinifera cultivars, we tested for genetic associations of these phenotypes using previously obtained genotyping data from the Vitis9kSNP array. We found one single nucleotide polymorphism (SNP) significantly associated with domatia density. This SNP (Chr5:1160194) is near two genes of interest: Importin Alpha Isoform 1 (VIT_205s0077g01440), involved in downy mildew resistance, and GATA Transcription Factor 8 (VIT_205s0077g01450), involved in leaf shape development. Our findings are among the first to examine the genomic regions associated with ecologically important plant traits that facilitate interactions with beneficial mites, and suggest promising candidate genes for breeding and genetic editing to increase naturally occurring predator-based defenses in grapevines.

scholarly journals Genome-Wide Association Study and Linkage Analysis of the Healthy Aging Index

2015 ◽  
Vol 70 (8) ◽  
pp. 1003-1008 ◽  
Author(s):  
Ryan L. Minster ◽  
Jason L. Sanders ◽  
Jatinder Singh ◽  
Candace M. Kammerer ◽  
M. Michael Barmada ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Association Study ◽  
Healthy Aging ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Aging Index ◽  
Genome Wide

A chemical genetic roadmap to improved tomato flavor

Science ◽  
2017 ◽  
Vol 355 (6323) ◽  
pp. 391-394 ◽  
Author(s):  
Denise Tieman ◽  
Guangtao Zhu ◽  
Marcio F. R. Resende ◽  
Tao Lin ◽  
Cuong Nguyen ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Sequencing ◽  
Molecular Breeding ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Chemical Genetic ◽  
Genome Wide ◽  
A Genome ◽  
Wild Accessions

Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavor-associated chemicals in 398 modern, heirloom, and wild accessions. A subset of these accessions was evaluated in consumer panels, identifying the chemicals that made the most important contributions to flavor and consumer liking. We found that modern commercial varieties contain significantly lower amounts of many of these important flavor chemicals than older varieties. Whole-genome sequencing and a genome-wide association study permitted identification of genetic loci that affect most of the target flavor chemicals, including sugars, acids, and volatiles. Together, these results provide an understanding of the flavor deficiencies in modern commercial varieties and the information necessary for the recovery of good flavor through molecular breeding.

scholarly journals Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.)

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1335
Author(s):  
Taeklim Lee ◽  
Kyung Do Kim ◽  
Ji-Min Kim ◽  
Ilseob Shin ◽  
Jinho Heo ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Leaf Shape ◽  
Ultraviolet B ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Glycine Max L

The depletion of the stratospheric ozone layer is a major environmental issue and has increased the dosage of ultraviolet-B (UV-B) radiation reaching the Earth’s surface. Organisms are negatively affected by enhanced UV-B radiation, and especially in crop plants this may lead to severe yield losses. Soybean (Glycine max L.), a major legume crop, is sensitive to UV-B radiation, and therefore, it is required to breed the UV-B-resistant soybean cultivar. In this study, 688 soybean germplasms were phenotyped for two categories, Damage of Leaf Chlorosis (DLC) and Damage of Leaf Shape (DLS), after supplementary UV-B irradiation for 14 days. About 5% of the germplasms showed strong UV-B resistance, and GCS731 was the most resistant genotype. Their phenotypic distributions showed similar patterns to the normal, suggesting UV-B resistance as a quantitative trait governed by polygenes. A total of 688 soybean germplasms were genotyped using the Axiom® Soya 180K SNP array, and a genome-wide association study (GWAS) was conducted to identify SNPs significantly associated with the two traits, DLC and DLS. Five peaks on chromosomes 2, 6, 10, and 11 were significantly associated with either DLC or DLS, and the five adjacent genes were selected as candidate genes responsible for UV-B resistance. Among those candidate genes, Glyma.02g017500 and Glyma.06g103200 encode cryptochrome (CRY) and cryptochrome 1 (CRY1), respectively, and are known to play a role in DNA repair during photoreactivation. Real-time quantitative RT-PCR (qRT-PCR) results revealed that CRY1 was expressed significantly higher in the UV-B-resistant soybean compared to the susceptible soybean after 6 h of UV-B irradiation. This study is the first GWAS report on UV-B resistance in soybean, and the results will provide valuable information for breeding UV-B-resistant soybeans in preparation for climate change.

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