scholarly journals Construction of a Single-Nucleotide Polymorphism Marker Based Quantitative Trait Loci Map and Validation of Resistance Loci to Bacterial Wilt (Ralstonia solanacearum) in Tomato

2019 ◽  
Author(s):  
Il Sheob Shin ◽  
Jung Ching Hsu ◽  
Shu Mei Huang ◽  
Jaw Rong Chen ◽  
Jaw Fen Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quantitative Trait Loci ◽  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Quantitative Trait ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Race 1 ◽  
Phylotype I

Bacterial wilt (BW), caused by Ralstonia solanacearum is one of the major biotic factors limiting tomato production in the humid tropics. Pyramiding of resistance genes through marker-assisted selection is an efficient way to develop durable BW resistant cultivars. Tomato line ‘Hawaii 7996’ (H7996) is a stable and robust resistance source against various R. solanacearum strains. Major BW resistance quantitative trait loci (QTLs) Bwr-12 and Bwr-6, and several minor or strain specific QTLs have been coarse-mapped in this line, but none has been fine-mapped and validated. The objective of the current study was to construct a high density genetic map using single-nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing, fine-map Bwr-12 and Bwr-6 and determine the effects of these QTLs using a near isogenic line (NIL) population. A high density genetic map using 1,604 SNP markers with an average distance of 0.82 cM was developed for 188 F9 recombinant inbred lines derived from the cross H7996 × WVa700. A total of seven QTLs associated with BW resistance to race 1-phylotype I or/and race 3-phylotype II strains were located on chromosomes 6 (Bwr-6.1, 6.2, 6.3 and 6.4) and 12 (Bwr-12.1, Bwr-12.2 and Bwr-12.3) with logarithm of odds (LOD) scores of 6.2-15.6 and 6.2-31.1, explaining 14.2-33.4% and 15.9-53.9% of the total phenotypic variation contributed from H7996, respectively. To validate the genetic effects of the two QTL regions, a set of 80 BC3F3 NILs containing different sections of Bwr-6 with or without Bwr-12 was phenotyped for disease severity after challenge with either race 1-phylotype I Pss4 or race 3-phylotype II Pss1632 BW strains over two seasons. Bwr-6.1 specific to Pss4 and Bwr-6.3 specific to Pss1632 were mapped to an interval of 5.0 cM (P < 0.05) between 6_33,444,000_SLM6-47 and 6_33,868,000_SLM6-124 SNP marker, and to 2.7 cM (P < 0.01) between positions 6_35,949,000 _SLM6-107 to 6_36,750,000_SLM6-82 marker, respectively. In addition, the specific effect of Bwr-12 for resistance to Pss4 (LOD score of 5.8-16.1, P < 0.01) was confirmed and markers for this QTL have already been made available previously.

The TG5 thyroglobulin gene test for a marbling quantitative trait loci evaluated in feedlot cattle

2004 ◽  
Vol 44 (7) ◽  
pp. 669 ◽  
Author(s):  
W. Barendse ◽  
R. Bunch ◽  
M. Thomas ◽  
S. Armitage ◽  
S. Baud ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quantitative Trait Loci ◽  
Dna Sequence ◽  
Dna Markers ◽  
Quantitative Trait ◽  
Allelic Association ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Thyroglobulin Gene

The TG5 (thyroglobulin 5′ leader sequence) single nucleotide polymorphism has been associated with marbling in cattle fed for periods longer than 250 days. To test whether the association could be detected in diverse cattle, fed for less than 250 days, and to measure the size of the effect, we sampled 1750 cattle from the AMH Toowoomba feedlot. These cattle were sampled on 28 separate days, over 9 months. Their marbling scores covered the complete range. We found that the TG5 single nucleotide polymorphism was associated with marbling scores (P<0.05) and estimated that TG5 genotypes explained 6.5% of the residual deviance for the marbling phenotype. We also found that the '3' allele was more frequent in animals with higher marbling scores. The consistency of the allelic association between studies and, in particular, the association found in diverse cattle, indicate that the TG5 polymorphism can be used as a breeding tool and possibly a feedlot entry tool. To estimate the size of the genetic region in which the marbling quantitative trait loci are located, we tested the nearby DNA markers CSSM66 and BMS1747. These do not show allelic associations to marbling. The consistency of the allelic association between studies, the lack of association to nearby DNA markers and the complementary information on gene action of genes near Thyroglobulin suggest that DNA sequence variations, in or near the Thyroglobulin gene sequence, are the likely causes for the marbling quantitative trait loci. Further studies of single nucleotide polymorphism in and near the Thyroglobulin DNA sequence should allow causal mutations for the effect to be identified.

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