Introgression of Maize Lethal Necrosis Resistance Quantitative Trait Loci Into Susceptible Maize Populations and Validation of the Resistance Under Field Conditions in Naivasha, Kenya

Maize lethal necrosis (MLN), resulting from co-infection by maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) can cause up to 100% yield losses in maize in Africa under serious disease conditions. Maize improvement through conventional backcross (BC) takes many generations but can significantly be shortened when molecular tools are utilized in the breeding process. We used a donor parent (KS23-6) to transfer quantitative trait loci (QTL) for resistance to MLN into nine adapted but MLN susceptible lines. Nurseries were established in Kiboko, Kenya during 2015–2017 seasons and BC3F2 progeny were developed using marker assisted backcrossing (MABC) approach. Six single nucleotide polymorphism (SNP) markers linked to QTL for resistance to MLN were used to genotype 2,400 BC3F2 lines using Kompetitive Allele Specific PCR (KASP) platform. We detected that two of the six QTL had major effects for resistance to MLN under artificial inoculation field conditions in 56 candidate BC3F2 lines. To confirm whether these two QTL are reproducible under different field conditions, the 56 BC3F2 lines including their parents were evaluated in replicated trials for two seasons under artificial MLN inoculations in Naivasha, Kenya in 2018. Strong association of genotype with phenotype was detected. Consequently, 19 superior BC3F2 lines with favorable alleles and showing improved levels of resistance to MLN under artificial field inoculation were identified. These elite lines represent superior genetic resources for improvement of maize hybrids for resistance to MLN. However, 20 BC3F2 lines were fixed for both KASP markers but were susceptible to MLN under field conditions, which could suggest weak linkage between the KASP markers and target genes. The validated two major QTL can be utilized to speed up the breeding process but additional loci need to be identified between the KASP markers and the resistance genes to strengthen the linkage.

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Diverse Chromosomal Locations of Quantitative Trait Loci for Tolerance to Maize chlorotic mottle virus in Five Maize Populations

Phytopathology ◽

10.1094/phyto-09-17-0321-r ◽

2018 ◽

Vol 108 (6) ◽

pp. 748-758 ◽

Cited By ~ 11

Author(s):

Mark W. Jones ◽

Bryan W. Penning ◽

Tiffany M. Jamann ◽

Jeff C. Glaubitz ◽

Cinta Romay ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Leaf Tissue ◽

Inbred Lines ◽

Mottle Virus ◽

Maize Populations ◽

Chlorotic Mottle Virus ◽

Maize Chlorotic Mottle Virus ◽

Chlorotic Mottle ◽

Trait Loci

The recent rapid emergence of maize lethal necrosis (MLN), caused by coinfection of maize with Maize chlorotic mottle virus (MCMV) and a second virus usually from the family Potyviridae, is causing extensive losses for farmers in East Africa, Southeast Asia, and South America. Although the genetic basis of resistance to potyviruses is well understood in maize, little was known about resistance to MCMV. The responses of five maize inbred lines (KS23-5, KS23-6, N211, DR, and Oh1VI) to inoculation with MCMV, Sugarcane mosaic virus, and MLN were characterized. All five lines developed fewer symptoms than susceptible controls after inoculation with MCMV; however, the virus was detected in systemic leaf tissue from each of the lines similarly to susceptible controls, indicating that the lines were tolerant of MCMV rather than resistant to it. Except for KS23-5, the inbred lines also developed fewer symptoms after inoculation with MLN than susceptible controls. To identify genetic loci associated with MCMV tolerance, large F2 or recombinant inbred populations were evaluated for their phenotypic responses to MCMV, and the most resistant and susceptible plants were genotyped by sequencing. One to four quantitative trait loci (QTL) were identified in each tolerant population using recombination frequency and positional mapping strategies. In contrast to previous studies of virus resistance in maize, the chromosomal positions and genetic character of the QTL were unique to each population. The results suggest that different, genotype-specific mechanisms are associated with MCMV tolerance in maize. These results will allow for the development of markers for marker-assisted selection of MCMV- and MLN-tolerant maize hybrids for disease control.

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Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions

Journal of Experimental Botany ◽

10.1093/jxb/err292 ◽

2011 ◽

Vol 63 (1) ◽

pp. 455-469 ◽

Cited By ~ 64

Author(s):

Junfei Gu ◽

Xinyou Yin ◽

Paul C. Struik ◽

Tjeerd Jan Stomph ◽

Huaqi Wang

Keyword(s):

Oryza Sativa ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Oryza Sativa L ◽

Introgression Lines ◽

Field Conditions ◽

Trait Loci ◽

Chromosome Introgression

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Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters

Genes ◽

10.3390/genes12071040 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1040

Author(s):

Kexin Zhang ◽

Jinpeng Wang ◽

Fangfang Ding ◽

Ruihui Shi ◽

Wei Wang ◽

...

Keyword(s):

Climate Change ◽

Gene Expression ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Target Genes ◽

Future Climate Change ◽

Climate Change Scenarios ◽

Expression Quantitative Trait Loci ◽

Independent Family ◽

Trait Loci

Many marine ectotherms, especially those inhabiting highly variable intertidal zones, develop high phenotypic plasticity in response to rapid climate change by modulating gene expression levels. Herein, we examined the regulatory architecture of heat-responsive gene expression plasticity in oysters using expression quantitative trait loci (eQTL) analysis. Using a backcross family of Crassostrea gigas and its sister species Crassostrea angulata under acute stress, 56 distant regulatory regions accounting for 6–26.6% of the gene expression variation were identified for 19 heat-responsive genes. In total, 831 genes and 164 single nucleotide polymorphisms (SNPs) that could potentially regulate expression of the target genes were screened in the eQTL region. The association between three SNPs and the corresponding target genes was verified in an independent family. Specifically, Marker13973 was identified for heat shock protein (HSP) family A member 9 (HspA9). Ribosomal protein L10a (RPL10A) was detected approximately 2 kb downstream of the distant regulatory SNP. Further, Marker14346-48 and Marker14346-85 were in complete linkage disequilibrium and identified for autophagy-related gene 7 (ATG7). Nuclear respiratory factor 1 (NRF1) was detected approximately 3 kb upstream of the two SNPs. These results suggested regulatory relationships between RPL10A and HSPA9 and between NRF1 and ATG7. Our findings indicate that distant regulatory mutations play an important role in the regulation of gene expression plasticity by altering upstream regulatory factors in response to heat stress. The identified eQTLs provide candidate biomarkers for predicting the persistence of oysters under future climate change scenarios.

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Mapping of quantitative trait loci associated with chilling tolerance in maize (Zea mays L.) seedlings grown under field conditions

Journal of Experimental Botany ◽

10.1093/jxb/eri108 ◽

2005 ◽

Vol 56 (414) ◽

pp. 1153-1163 ◽

Cited By ~ 52

Author(s):

Choosak Jompuk ◽

Yvan Fracheboud ◽

Peter Stamp ◽

Jörg Leipner

Keyword(s):

Zea Mays ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Zea Mays L ◽

Chilling Tolerance ◽

Field Conditions ◽

Trait Loci

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Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.796189 ◽

2022 ◽

Vol 12 ◽

Author(s):

Yijing Gao ◽

Shan Zhou ◽

Yuxin Huang ◽

Baoqing Zhang ◽

Yuhui Xu ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Rna Sequencing ◽

Genetic Map ◽

Quantitative Trait ◽

Resistance Breeding ◽

Phenotypic Variance ◽

Screening Assay ◽

Major Qtls ◽

Trait Loci ◽

Kasp Markers

Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called “specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.

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Quantitative trait loci for resistance to fusarium head blight and deoxynivalenol accumulation in Wangshuibai wheat under field conditions

Plant Pathology ◽

10.1111/j.1365-3059.2006.01447.x ◽

2006 ◽

Vol 55 (6) ◽

pp. 739-745 ◽

Cited By ~ 39

Author(s):

H. X. Ma ◽

K. M. Zhang ◽

L. Gao ◽

G. H. Bai ◽

H. G. Chen ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Fusarium Head Blight ◽

Quantitative Trait ◽

Field Conditions ◽

Head Blight ◽

Trait Loci

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Quantitative trait loci for seedling vigor in rice under field conditions

Field Crops Research ◽

10.1016/j.fcr.2006.08.003 ◽

2007 ◽

Vol 100 (2-3) ◽

pp. 294-301 ◽

Cited By ~ 43

Author(s):

Liang Zhou ◽

Jin-Kai Wang ◽

Qiong Yi ◽

Yi-Zhong Wang ◽

Ying-Guo Zhu ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Field Conditions ◽

Seedling Vigor ◽

Trait Loci

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Identification of quantitative trait loci and the exploration of candidate genes for the tolerance to Zn deficiency in maize

10.21203/rs.2.12668/v1 ◽

2019 ◽

Author(s):

Jianqin Xu ◽

Xiaoyang Zhu ◽

Xiuyi Fu ◽

Futong Yu

Keyword(s):

Quantitative Trait Loci ◽

Candidate Genes ◽

Quantitative Trait ◽

Genetic Basis ◽

Target Genes ◽

Functional Characterization ◽

Chromosome 1 ◽

Zn Deficiency ◽

Homologous Gene ◽

Trait Loci

Abstract Background Zn is essential for plants and Zn deficiency leads to great reduction in quality and quantity of crops. Maize, as one of the most important main staple crops worldwide, is more susceptible to Zn deficiency than any other cereal crops. Therefore, understanding the functional mechanisms in tolerance to Zn deficiency in maize is urgent but is still lacking. In this study, quantitative trait loci (QTL) analysis in K22 and By815 RIL population with high-density bin map was conducted to investigate genetic basis of the mechanisms in maize to tolerate Zn deficiency, subsequently some candidate genes were identified and considered as being associated with Zn metabolisms in plants. Results 21 QTLs were detected and accounted for 5.9% - 16.6% of phenotypic variations. Based on the co-localization in this study and the comparisons with previous studies in different RIL and GWAS populations, 223 candidate genes were identified inside the reduced QTL peak intervals on chromosome 1, 2, 6, 7 and 9. Furthermore, 9 genes detected within the peak bins of valuable genomic regions are suggested to be associated with ions transportation and some redox processes affected by Zn deficiency. Additionally, 5 genes, including ZmIRT1, ZmNRAMP6, ZmEIN2 and ZmHMAs, whose homologous gene have been studied and considered to be responsible for metal cations transportation and ethylene-signaling pathway requiring a transition metal were discovered in 5 loci we mapped. Conclusions 14 target genes identified in 9 loci we mapped in this work were explored to elucidate the potential functions in Zn homeostasis and the direct or indirect effects on mechanisms in Zn deficiency tolerance in maize. It is the first time that ZmIRT1, ZmNRAMP6, ZmHMAs were identified using linkage analysis under Zn deficiency in maize, providing genetic evidence and foundation for further gene functional characterization. Our findings have assisted us untangling the genetic basis of possible mechanisms in response to Zn deficiency in maize.

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High-Resolution Detection of Quantitative Trait Loci for Seven Important Yield Components in Wheat (Triticum aestivum L.) using a High-Density SALF-Seq Genetic Map

10.21203/rs.3.rs-783221/v1 ◽

2021 ◽

Author(s):

Tao Li ◽

Qiao Li ◽

Jinhui Wang ◽

Zhao Yang ◽

Yanyan Tang ◽

...

Keyword(s):

Triticum Aestivum ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Expression Patterns ◽

Phenotypic Variance ◽

Wheat Varieties ◽

Major Qtls ◽

Grain Number Per Spike ◽

Trait Loci ◽

Kasp Markers

Abstract Background: Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with wheat (Triticum aestivum L.) grain yield. To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six or eight environments. Results: A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multiple environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked to five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search. Conclusions: Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grian yield and developing new wheat varieties with high and stable yield in wheat.

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