scholarly journals Genotyping by sequencing of 393 Sorghum bicolor BTx623 × IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection

2018 ◽  
Author(s):  
WenQian Kong ◽  
Changsoo Kim ◽  
Dong Zhang ◽  
Hui Guo ◽  
Xu Tan ◽  
...  
Keyword(s):  
Flowering Time ◽  
Plant Height ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Ril Population ◽  
Trait Locus ◽  
Number Of Individuals ◽  
Syntenic Regions

AbstractWe describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)-based SNP markers in a F6-F8 recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTLs relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTLs for each trait and provide evidence against pleiotropy. Ten non-random syntenic regions conferring QTLs for the same trait suggest that those QTLs may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTLs for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.

scholarly journals Morphological Trait QTL Mapping in Tomato Recombinant Inbred Line Population

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 788D-788
Author(s):  
I. Paran ◽  
I.L. Goldman ◽  
D. Zamir
Keyword(s):  
Plant Height ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Morphological Traits ◽  
Recombinant Inbred Lines ◽  
Rflp Analysis ◽  
Leaf Length ◽  
Node Number ◽  
Marker Loci ◽  
Trait Locus

Quantitative trait loci influencing morphological traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RIL) derived from a cross of the cultivated tomato (Lycopersicon esculentum) with a related wild species (L. cheesmanii). One-hundred-thirty-two polymorphic RFLP loci spaced throughout the tomato genome were scored for 97 RIL families. Morphological traits, including plant height, fresh weight, node number, first flower-bearing node, leaf length at nodes three and four, and number of branches, were measured in replicated trials during 1991, 1992, and 1993. Significant (P ≤ 0.01 level) quantitative trait locus (QTL) associations of marker loci were identified for each trait. Lower plant height, more branches, and shorter internode length were generally associated with RFLP alleles from the L. cheesmanii parent. QTL with large effects on a majority of the morphological traits measured were detected at chromosomes 2, 3, and 4. Large additive effects were measured at significant marker loci for many of the traits measured. Several marker loci exhibited significant associations with numerous morphological traits, suggesting their possible linkage to genes controlling growth and development processes in Lycopersicon.

Mapping QTLs for plant height and flowering time in a Chinese summer planting soybean RIL population

Euphytica ◽  
2017 ◽  
Vol 213 (2) ◽  
Author(s):  
Yongce Cao ◽  
Shuguang Li ◽  
Xiaohong He ◽  
Fangguo Chang ◽  
Jiejie Kong ◽  
...  
Keyword(s):  
Flowering Time ◽  
Plant Height ◽  
Ril Population

scholarly journals Population Structure and Association Analysis of Bolting, Plant Height, and Leaf Erectness in Spinach

HortScience ◽  
2016 ◽  
Vol 51 (5) ◽  
pp. 481-486 ◽  
Author(s):  
Jessica Chitwood ◽  
Ainong Shi ◽  
Beiquan Mou ◽  
Michael Evans ◽  
John Clark ◽  
...  
Keyword(s):  
Linear Model ◽  
Plant Height ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Structured Populations ◽  
United States Department ◽  
Nucleotide Polymorphisms ◽  
Single Marker

Spinach (Spinacia oleracea L.) is an important vegetable worldwide with high nutritional and health-promoting compounds. Bolting is an important trait to consider to grow spinach in different seasons and regions. Plant height and leaf erectness are important traits for machine harvesting. Breeding slow bolting, taller, and more erect spinach cultivars is needed for improved spinach production. A total of 288 United States Department of Agriculture (USDA) spinach accessions were used as the association panel in this research. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Two structured populations and the admixtures were inferred for the 288 spinach accession panel using STRUCTURE and MEGA. Association mapping was conducted using single-marker regression (SMR) in QGene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. Three SNP markers, AYZV02001321_398, AYZV02041012_1060, and AYZV02118171_95 were identified to be associated with bolting. Eight SNP markers, AYZV02014270_540, AYZV02250508_2162, AYZV02091523_19842, AYZV02141794_376, AYZV02077023_64, AYZV02210662_2532, AYZV02153224_2197, and AYZV02003975_248 were found to be associated with plant height. Four SNP markers, AYZV02188832_229, AYZV02219088_79, AYZV02030116_256, and AYZV02129827_197 were associated with erectness. These SNP markers may provide breeders with a tool in spinach molecular breeding to select spinach bolting, plant height, and erectness through marker-assisted selection (MAS).

scholarly journals Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1690
Author(s):  
Yheni Dwiningsih ◽  
Anuj Kumar ◽  
Julie Thomas ◽  
Charles Ruiz ◽  
Jawaher Alkahtani ◽  
...  
Keyword(s):  
Candidate Genes ◽  
High Throughput ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Genetic Information ◽  
Snp Markers ◽  
Rice Grain ◽  
Grain Length ◽  
Ril Population

Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of “Kaybonnet (KBNT lpa)” and “ZHE733” named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.

scholarly journals Genome-Wide Association Mapping of Resistance to the Sugarcane Aphid in Sorghum bicolor

2021 ◽  
Author(s):  
Somashekhar Punnuri ◽  
Addissu Ayele ◽  
Karen Harris-Shultz ◽  
Joseph Knoll ◽  
Alisa Coffin ◽  
...  
Keyword(s):  
Flowering Time ◽  
Plant Height ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Aphid Resistance ◽  
Melanaphis Sacchari ◽  
Phenotypic Data ◽  
Sugarcane Aphid ◽  
Genome Wide ◽  
Sorghum Production

Abstract Since 2013, the sugarcane aphid (SCA), Melanaphis sacchari (Zehntner), has been a serious pest that hampers all types of sorghum production in the U.S. Our understanding of sugarcane aphid resistance in sorghum is limited to knowledge about a few genetic regions on chromosome SBI-06. In this study, a subset of the Sorghum Association Panel (SAP) was used along with some additional lines to identify genetic and genomic regions that confer sugarcane aphid resistance. SAP lines were grown in the field and visually evaluated for SCA resistance during the growing seasons of 2019 and 2020 in Tifton, GA. In 2020, the SAP accessions were also evaluated for SCA resistance in the field using drone-based high throughput phenotyping (HTP) and visual scoring under greenhouse conditions. Plant height and flowering time were also recorded in the field to confirm that our methods were sufficient for identifying known quantitative trait loci (QTL). This study combined phenotypic data from field-based visual ratings, reflectance data, and greenhouse evaluations to identify genome-wide associated (GWAS) marker-trait associations (MTA) using genotyping-by-sequencing (GBS) data. Several MTAs were identified for sugarcane aphid-related traits across the genome, with a few common markers that were consistently identified on SBI-08 and SBI-10 for aphid count and plant damage as well as for reflectance indices-based traits on SBI-02, SBI-03, and SBI-05. Candidate genes encoding leucine-rich repeats (LRR), Avr proteins, lipoxygenases (LOXs), calmodulins (CAM) dependent protein kinase, WRKY transcription factors, flavonoid biosynthesis genes, and 12-oxo-phytodienoic acid reductase are identified near SNPs that had significant associations with different SCA traits. In this study, plant height and flowering time-related genes were also identified. The total phenotypic variation explained by significant SNPs across SCA-scored traits, plant height, and flowering time ranged from 0 to 74%, while the heritability value ranged from 4 to 74%. These results supported the existing literature, and also revealed several new loci. Markers identified in this study will support marker-assisted breeding for sugarcane aphid resistance.

scholarly journals GRAS-Di system facilitates high-density genetic map construction and QTL identification in recombinant inbred lines of the wheat progenitor Aegilops tauschii

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yuka Miki ◽  
Kentaro Yoshida ◽  
Hiroyuki Enoki ◽  
Shoya Komura ◽  
Kazuyo Suzuki ◽  
...  
Keyword(s):  
Flowering Time ◽  
Genetic Markers ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Aegilops Tauschii ◽  
Amplicon Sequencing ◽  
Inbred Lines ◽  
High Density ◽  
D Genome ◽  
Triticeae Species

AbstractDue to large and complex genomes of Triticeae species, skim sequencing approaches have cost and analytical advantages for detecting genetic markers and building linkage maps. Here, we develop a high-density linkage map and identify quantitative trait loci (QTLs) for recombinant inbred lines of Aegilops tauschii, a D-genome donor of bread wheat, using the recently developed genotyping by Random Amplicon Sequencing-Direct (GRAS-Di) system, which facilitates skimming of the large and complicated genome and generates a large number of genetic markers. The deduced linkage groups based on the GRAS-Di genetic markers corresponded to the chromosome number of Ae. tauschii. We successfully identified stable QTLs for flowering time and spikelet shape-related traits. Genotype differences of RILs at the QTL-linked markers were significantly associated with the trait variations. In particular, one of the QTL-linked markers for flowering time was mapped close to VRN3 (also known as FLOWERING LOCUS T), which controls flowering. The GRAS-Di system is, therefore, an efficient and useful application for genotyping and linkage mapping in species with large and complex genomes, such as Triticeae species.

scholarly journals Mapping QTLs for protein and oil content in soybean by removing the influence of related traits in a four-way recombinant inbred line population

2019 ◽  
Vol 157 (9-10) ◽  
pp. 659-675 ◽  
Author(s):  
Xiyu Li ◽  
Hong Xue ◽  
Kaixin Zhang ◽  
Wenbin Li ◽  
Yanlong Fang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Recombinant Inbred ◽  
Oil Content ◽  
Molecular Breeding ◽  
Recombinant Inbred Lines ◽  
Interval Mapping ◽  
Inbred Lines ◽  
Additive Effects ◽  
Linkage Maps ◽  
Trait Locus

AbstractProtein content (PC) and oil content (OC) are important breeding traits of soybean [Glycine max (L.) Merr.]. Quantitative trait locus (QTL) mapping for PC and OC is important for molecular breeding in soybean; however, the negative correlation between PC and OC influences the accuracy of QTL mapping. In the current study, a four-way recombinant inbred lines (FW-RILs) population comprising 160 lines derived from the cross (Kenfeng14 × Kenfeng15) × (Heinong48 × Kenfeng19) was planted in eight different environments and PC and OC measured. Conditional and unconditional QTL analyses were carried out by interval mapping (IM) and inclusive complete IM based on linkage maps of 275 simple sequences repeat markers in a FW-RILs population. This analysis revealed 59 unconditional QTLs and 52 conditional QTLs among the FW-RILs. An analysis of additive effects indicated that the effects of 13 protein QTLs were not related to OC, whereas OC affected the expression of 13 and eight QTLs either partially or completely, respectively. Eight QTLs affecting OC were not influenced by PC, whereas six and 26 QTLs were partially and fully affected by PC, respectively. Among the QTLs detected in the current study, two protein QTLs and five oil QTLs had not been previously reported. These findings will facilitate marker-assisted selection and molecular breeding of soybean.

scholarly journals Genetic Analysis of Recombinant Inbred Lines for Sorghum bicolor × Sorghum propinquum

2013 ◽  
Vol 3 (1) ◽  
pp. 101-108 ◽  
Author(s):  
Wenqian Kong ◽  
Huizhe Jin ◽  
Cleve D Franks ◽  
Changsoo Kim ◽  
Rajib Bandopadhyay ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Sorghum Bicolor ◽  
Genetic Map ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Growth And Development ◽  
Recombinant Inbred Lines ◽  
Sorghum Propinquum ◽  
Ril Population ◽  
Trait Loci

Abstract We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor × Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor × S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map has DNA marker density well-suited to quantitative trait loci mapping and samples most of the genome, our previous observations that sorghum pericentromeric heterochromatin is recalcitrant to recombination is highlighted by the finding that the vast majority of recombination in sorghum is concentrated in small regions of euchromatin that are distal to most chromosomes. The advancement of the RIL population in an environment to which the S. bicolor parent was well adapted (indeed bred for) but the S. propinquum parent was not largely eliminated an allele for short-day flowering that confounded many other traits, for example, permitting us to map new quantitative trait loci for flowering that previously eluded detection. Additional recombination that has accrued in the development of this RIL population also may have improved resolution of apices of heterozygote excess, accounting for their greater abundance in the F5 than the F2 generation. The S. bicolor × S. propinquum RIL population offers advantages over early-generation populations that will shed new light on genetic, environmental, and physiological/biochemical factors that regulate plant growth and development.

Genetic resolution and verification of quantitative trait loci for flowering and plant height with recombinant inbred lines of maize

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 957-968 ◽  
Author(s):  
David F. Austin ◽  
Michael Lee
Keyword(s):  
Quantitative Trait Loci ◽  
Plant Height ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Length Polymorphisms ◽  
Trait Loci ◽  
Ear Height ◽  
Single Factor Analysis

Recombinant inbred (RI) lines offer several advantages for detecting quantitative trait loci (QTLs), including increased precision of trait measurements, power for detection of additive effects, and resolution of linked QTLs. This study was conducted to detect and characterize QTLs in maize for flowering and plant height and to compare QTL detection in an early (F2:3) generation of the same population. One hundred and eighty-six RIs from a cross between inbred lines Mo17 and H99 were evaluated in a replicated field experiment and analyzed at 101 loci detected by restriction fragment length polymorphisms. QTLs were identified by single-factor analysis of variance. A total of 59 QTLs were detected for plant height, ear height, top height, anthesis, silk emergence, and anthesis to silk interval. Individual QTLs explained 2.2–15.4% of trait variation, and multiple models including all QTLs detected for a trait explained up to 52.5% of the phenotypic variation. Comparison of QTLs detected with 150 F2:3 lines from the same population indicated that 16 (70%) of the 23 F2:3 QTLs were also observed in the F6:7 generation. Parental effects were consistent across generations. At 14 of the 16 QTLs detected in both generations, genetic effects were smaller in the F6:7. Also, some QTLs detected in the F2:3 were resolved into multiple linked QTLs in the F6:7, indicating the additional power of RI populations for mapping, with important implications for marker-assisted selection as well as map-based cloning of QTLs. Key words : Zea mays, RFLP, plant breeding, genetics, recombination.

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