scholarly journals Fine Mapping and Candidate Gene Analysis of the Up Locus Determining Fruit Orientation in Pepper (Capsicum spp.)

2021 ◽  
Author(s):  
Fang Hu ◽  
Jiaowen Cheng ◽  
Jichi Dong ◽  
Jian Zhong ◽  
Ziyan Zhou ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Sequence Comparison ◽  
Dominant Gene ◽  
Gene Isolation ◽  
Recurrent Parent ◽  
Wild Relative ◽  
Developmentally Regulated ◽  
Backcross Population ◽  
Capsicum Spp ◽  
Major Qtl

Abstract Fruit orientation is an important horticultural and domesticated trait, which is controlled by a single semi-dominant gene (up) in pepper. However, the gene underlying up locus has not yet been identified. In this study, the previously detected major QTL UP12.1 was firstly verified using an intraspecific backcross population (n=225) stem from the cross of BB3 (C. annuum) and its wild relative Chiltepin (C. annuum var. glabriusculum) using BB3 as the recurrent parent. Then, a large BC1F2 population (n=1827) was used for recombinant screening to delimit the up locus into an interval with ~169.51 kb in length. Sequence comparison and expression analysis suggested that Capana12g000958, encoding a developmentally regulated G-protein 2, was the most likely candidate gene for up. The findings of this study will form a basis for gene isolation and reveal of genetic mechanism underlying the fruit orientation domestication in pepper.

scholarly journals QTL analysis and fine mapping of a major QTL conferring kernel size in maize (Zea mays)

2020 ◽  
Author(s):  
Guiying Wang ◽  
Yanming Zhao ◽  
Zhen Zhu ◽  
Xinyuan Zhang ◽  
Minghua Jiang ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Linkage Map ◽  
Fine Mapping ◽  
Marker Assisted Selection ◽  
Chromosome 9 ◽  
Recurrent Parent ◽  
Kernel Size ◽  
Kernel Length ◽  
Stable Qtls ◽  
Major Qtl

Abstract Background：Kernel size are important agronomic traits for grain yield in maize. The objective of this study is to map QTLs for kernel size, fine map a stable QTL qKL-2 and predict candidate genes for kernel length in maize. A total 199 F2:3 lines were obtained from selfing F2 individuals from the cross SG5/SG7. In this study, a high density genetic linkage map with 3305 bin-markers spanning a total length of 2236.66 cM on 10 chromosomes was applied for primary QTL mapping. Composite interval mapping (CIM) method was used for detecting QTLs in three environments of F2 and F2:3 populations. Results：The result showed that a total ten QTLs for kernel size were detected, among which five QTLs for kernel length (KL) and five QTLs for kernel width (KW). Two stable QTLs qKW-1 and qKL-2 were mapped in all three environments. In order to validate and fine map qKL-2 , near isogenic lines (NILs) were developed by continuous backcross between SG5 as the donor parent and SG7 as the recurrent parent. Marker assisted selection was conducted from BC2F1 generation with molecular markers near qKL-2. Secondary linkage map with six markers around the objective region was developed for fine mapping qKL-2. Finally, qKL-2 was mapped in a 1.95Mb physical interval on maize chromosome 9 by blasting with Zea_Mays_B73 v4 genome. The results were confirmed with selected overlapping recombinant chromosomes. A total 11 out of 40 protein coding genes in the identified interval differentially expressed after conducting transcriptomic analysis between the two parents. GRMZM2G006080, which encodes receptor-like protein kinase FERONIA was predicted as candidate gene to control kernel size. Conclusions：A total ten QTLs for kernel size were identified. Two stable QTLs qKL-2 and qKW-2 were mapped in three envionments. Major QTL qKL-2 for KL was validated and fine mapped in a 1.95Mb physical interval. GRMZM2G006080 was predicted as candidate gene for qKL-2 to control kernel length. The work will not only help to understand the mechanisms that control kernel size of maize, but also provide new gene for marker-assisted selection in further studies.

Linkage mapping in diploid alfalfa (Medicago sativa)

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 61-71 ◽  
Author(s):  
C. S. Echt ◽  
K. K. Kidwell ◽  
S. J. Knapp ◽  
T. C. Osborn ◽  
T. J. McCoy
Keyword(s):  
Linkage Map ◽  
Linkage Mapping ◽  
Rapd Markers ◽  
Genome Mapping ◽  
Recurrent Parent ◽  
Backcross Population ◽  
Length Polymorphisms ◽  
Combined Use ◽  
A Genome ◽  
Genome Map

A genome map of cultivated alfalfa was constructed using segregating restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs) in a diploid backcross population generated from noninbred parents. Among the 153 loci scored in 87 progeny, four segregation ratios were observed for codominant and dominant markers: 1:1, 1:2:1, 1:1:1:1, and 3:1. Deviations from expected Mendelian ratios (p < 0.05) were observed for 34% of the loci studied. A genome map was assembled from two separate linkage maps, each constructed from a subset of the segregation data. One linkage map was constructed from 46 RFLP and 40 RAPD markers segregating 1:1 from the F1 parent of the backcross and the other linkage map was constructed from 33 RFLP and 28 RAPD markers segregating 1:1 from the recurrent parent. Sixteen loci with alleles segregating 1:1 from both parents were used as locus bridges to align individual linkage groups between the two maps. The combined use of RFLPs and RAPDs was an effective method for developing an alfalfa genome map.Key words: genome mapping, RAPD, RFLP, locus bridges.

scholarly journals Effect of gibberellin-sensitive Rht18 and gibberellin-insensitive Rht-D1b dwarfing genes on vegetative and reproductive growth in bread wheat

2020 ◽  
Author(s):  
Ting Tang ◽  
Tina Botwright Acuña ◽  
Wolfgang Spielmeyer ◽  
Richard A Richards
Keyword(s):  
Dry Matter ◽  
Green Revolution ◽  
Dominant Gene ◽  
Early Growth ◽  
Wheat Breeding ◽  
Dwarfing Genes ◽  
Coleoptile Length ◽  
Backcross Population ◽  
Wheat Improvement ◽  
Vegetative And Reproductive Growth

Abstract Gibberellin (GA)-insensitive dwarfing genes Rht-B1b and Rht-D1b that are responsible for the ‘Green Revolution’ have been remarkably successful in wheat improvement globally. However, these alleles result in shorter coleoptiles and reduced vigour, and hence poor establishment and growth in some environments. Rht18, on the other hand, is a GA-sensitive, dominant gene with potential to overcome some of the early growth limitations associated with Rht-B1b and Rht-D1b. We assessed progeny from both a biparental and a backcross population that contained tall, single dwarf, and double dwarf lines, to determine whether Rht18 differs from Rht-D1b and hence verify its value in wheat improvement. Progeny with Rht18 had an almost identical height to lines with Rht-D1b, and both were ~26% shorter than the tall lines, with the double dwarf 13% shorter again. However, coleoptile length of Rht18 was 42% longer than that of Rht-D1b. We detected no differences in time to terminal spikelet and anthesis, and few differences in stem or spike growth. Both dwarfing genes diverted more dry matter to the spike than tall lines from prior to heading. No differences were detected between Rht18 and Rht-D1b that could prevent the adoption of Rht18 in wheat breeding to overcome some of the limitations associated with the ‘Green Revolution’ genes.

scholarly journals Molecular Mapping of YrSP and Its Relationship with Other Genes for Stripe Rust Resistance in Wheat Chromosome 2BL

2015 ◽  
Vol 105 (9) ◽  
pp. 1206-1213 ◽  
Author(s):  
J. Y. Feng ◽  
M. N. Wang ◽  
X. M. Chen ◽  
D. R. See ◽  
Y. L. Zheng ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Chromosomal Location ◽  
Molecular Mapping ◽  
Puccinia Striiformis ◽  
Dominant Gene ◽  
The United States ◽  
Stripe Rust Resistance ◽  
Recurrent Parent ◽  
Isogenic Line ◽  
Sts Markers

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. Resistance is the best way to control the disease. YrSP, a gene originally from ‘Spaldings Prolific’ wheat and providing resistance to a broad spectrum of races, is used for differentiating P. striiformis f. sp. tritici races but its chromosomal location is not clear. To map YrSP, a near-isogenic line (AvSYrSPNIL) was backcrossed to the recurrent parent, Avocet S. Genetic analysis of the BC7F1, BC8, BC7F2, and BC7F3 progenies confirmed a single dominant gene for resistance. In total, 182 BC7F2 plants and their derived BC7F3 lines were phenotyped with an avirulent P. striiformis f. sp. tritici race and genotyped with simple-sequence repeat (SSR), single-nucleotide polymorphism (SNP), and sequence-tagged site (STS) markers. A linkage map was constructed with 3 SSR, 17 SNP, and 3 STS markers covering 23.3 centimorgans (cM). Markers IWA638 and dp269 were 0.6 cM proximal and 1.5 cM distal, respectively, to YrSP. The gene was mapped in chromosome bin 2BL-C-0.5, physically within the proximal 50% of the chromosome 2BL arm. Allelism tests based on F2 phenotypes indicated that YrSP is closely linked to but not allelic with genes Yr5, Yr7, Yr43, Yr44, and Yr53. Infection type data from tests with 10 historical and currently predominant P. striiformis f. sp. tritici races in the United States also demonstrated differences in specificity between YrSP and the other genes. The specificity of YrSP is useful in differentiating P. striiformis f. sp. tritici races and studying the plant–pathogen interactions, and the information of chromosomal location of the gene and its tightly linked markers should be useful in developing resistant cultivars when combined with other genes for resistance to stripe rust.

Genetic Loci Controlling Lethal Cell Death in Tomato Caused by Viral Satellite RNA Infection

2012 ◽  
Vol 25 (8) ◽  
pp. 1034-1044 ◽  
Author(s):  
Ping Xu ◽  
Hua Wang ◽  
Frank Coker ◽  
Jun-ying Ma ◽  
Yuhong Tang ◽  
...  
Keyword(s):  
Cell Death ◽  
In Situ Hybridization ◽  
Programmed Cell Death ◽  
Minus Strand ◽  
Satellite Rna ◽  
Dominant Trait ◽  
Systemic Necrosis ◽  
Backcross Population ◽  
Major Qtl

Cucumber mosaic virus (CMV) associated with D satellite RNA (satRNA) causes lethal systemic necrosis (LSN) in tomato (Solanum lycopersicum), which involves programmed cell death. No resistance to this disease has been found in tomato. We obtained a line of wild tomato, S. habrochaitis, with a homogeneous non-lethal response (NLR) to the infection. This line of S. habrochaitis was crossed with tomato to generate F1 plants that survived the infection with NLR, indicating that NLR is a dominant trait. The NLR trait was successfully passed on to the next generation. The phenotype and genotype segregation was analyzed in the first backcross population. The analyses indicate that the NLR trait is determined by quantitative trait loci (QTL). Major QTL associated with the NLR trait were mapped to chromosomes 5 and 12. Results from Northern blot and in situ hybridization analyses revealed that the F1 and S. habrochaitis plants accumulated minus-strand satRNA more slowly than tomato, and fewer vascular cells were infected. In addition, D satRNA-induced LSN in tomato is correlated with higher accumulation of the minus-strand satRNA compared with the accumulation of the minus strand of a non-necrogenic mutant D satRNA.

scholarly journals Fine-Mapping And Identification of A Candidate Gene Controlling Seed Coat Color In Melon (Cucumis Melo L. Var. Chinensis Pangalo)

2021 ◽  
Author(s):  
Zhicheng Hu ◽  
Xueyin Shi ◽  
Xuemiao Chen ◽  
Jing Zheng ◽  
Aiai Zhang ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Seed Coat ◽  
Coat Color ◽  
Bulked Segregant Analysis ◽  
Dominant Gene ◽  
Seed Coat Color ◽  
Gene Encoding ◽  
Yellow Seed ◽  
Homeobox Protein ◽  
Yellow Seed Coat

Abstract Seed coat color is related to flavonoid content which is closely related to seed dormancy. According to the genetic analysis of a six-generation population derived from two parents (IC2508 with a yellow seed coat and IC2518 with a brown seed coat), we discovered that the yellow seed coat trait in melon was controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene was located at 11,860,000–15,890,000 bp (4.03 Mb) on Chr 6. The F2 population was genotyped using insertion-deletions (InDels), from which cleaved amplified polymorphic sequence (dCAPS) markers were derived to construct a genetic map. The gene was then fine-mapped to a 233.98 kb region containing 12 genes. Based on gene sequence analysis with two parents, we found that the MELO3C019554 gene encoding a homeobox protein (PHD transcription factor) had a nonsynonymous single nucleotide polymorphism (SNP) mutation in the coding sequence (CDS), and the SNP mutation resulted in the conversion of an amino acid (A→T) at residue 534. In addition, MELO3C019554 exhibited lower relative expression levels in the yellow seed coat than in the brown seed coat. Furthermore, we found that MELO3C019554 was related to 12 flavonoid metabolites. Thus, we predicted that MELO3C019554 is a candidate gene controlling seed coat color in melon. The study lays a foundation for further cloning projects and functional analysis of this gene, as well as marker-assisted selection breeding.

scholarly journals Low Correlation Between Genomic and Morphological Introgression Estimates in a Walnut Backcross

1998 ◽  
Vol 123 (2) ◽  
pp. 258-263 ◽  
Author(s):  
Keith Woeste ◽  
Gale McGranahan ◽  
Robert Bernatzky
Keyword(s):  
Fragment Length Polymorphism ◽  
Parental Species ◽  
Juglans Regia ◽  
Linkage Data ◽  
Recurrent Parent ◽  
Morphological Similarity ◽  
Randomly Amplified Polymorphic Dna ◽  
Backcross Population ◽  
Juglans Hindsii ◽  
Genomic Introgression

A first backcross population of walnuts {[Juglans hindsii (Jeps.) Jeps. × Juglans regia L.] × J. regia} was used to evaluate the correlation between morphological (statistical) and genetic distance during introgression. Five traits based on leaf morphology were identified to quantitate the morphology of the parental species, their F1 hybrids, and the backcrosses to each parent. These traits were used to evaluate the morphological similarity of first backcrosses to J. regia using Mahalanobis' distance. The amount of genomic introgression of each backcross was estimated using 59 randomly amplified polymorphic DNA (RAPD) and 41 restriction fragment-length polymorphism (RFLP) genetic markers that identify polymorphisms between J. regia and J. hindsii. A smaller scaffold set of markers was also identified using published linkage data. The correlation between the measures of morphological and genomic introgression for the first backcrosses was low (0.23) but significant. The results suggest that selection based on morphology during backcrossing will not be an effective way to recover recurrent parent genome.

scholarly journals Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pingyong Wang ◽  
Xiaojun Xu ◽  
Guangwei Zhao ◽  
Yuhua He ◽  
Chong Hou ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Cucumis Melo ◽  
Bulked Segregant Analysis ◽  
Phytophthora Capsici ◽  
Expression Patterns ◽  
Dominant Gene ◽  
Resistance Mechanism ◽  
Receptor Kinase ◽  
Caps Marker ◽  
Mutation Site

AbstractPhytophthora blight is one of the most serious diseases affecting melon (Cucumis melo) production. Due to the lack of highly resistant germplasms, the progress on disease-resistant research is slow. To understand the genetics of melon resistance to Phytophthora capsici, an F2 population containing 498 individuals was developed by crossing susceptible line E31 to highly resistant line ZQK9. Genetic analysis indicated that the resistance in ZQK9 was controlled by a dominant gene, tentatively named MePhyto. Through bulked-segregant analysis (BSA-Seq) and chromosome walking techniques, the MePhyto gene was mapped to a 52.44 kb interval on chromosome 12. In this region, there were eight genes and their expression patterns were validated by qRT-PCR. Among them, one wall-associated receptor kinase (WAK) gene MELO3C002430 was significantly induced in ZQK9 after P. capsici inoculation, but not in E31. Based on the non-synonymous mutation site in MELO3C002430, a cleaved amplified polymorphic sequence (CAPS) marker, CAPS2430, was developed and this maker was co-segregated with MePhyto in both F2 population and a collection of 36 melon accessions. Thus MELO3C002430 was considered as the candidate gene and CAPS2430 was a promising marker for marker-assisted selection (MAS) in breeding. These results lay a foundation for revealing the resistance mechanism of melon to P. capsici.

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