Genome-wide identification of quantitative trait loci for important plant and flower traits in petunia using a high-density linkage map and an interspecific recombinant inbred population derived from Petunia integrifolia and P. axillaris

AbstractHigh-density genetic map and quantitative trait loci (QTL) mapping are powerful tools for identifying genomic regions that may be responsible for such polygenic trait as growth. A high-density genetic linkage map was constructed by sequencing 198 individuals in a F1 family of silver carp (Hypophthalmichthys molitrix) in this study. This genetic map spans a length of 2,721.07 cM with 3,134 SNPs distributed on 24 linkage groups (LGs). Comparative genomic mapping presented a high level of syntenic relationship between silver carp and zebrafish. We detected one major and nineteen suggestive QTL for 4 growth-related traits (body length, body height, head length and body weight) at 6, 12 and 18 months post hatch (mph), explaining 10.2~19.5% of phenotypic variation. All six QTL for growth traits of 12 mph generally overlapped with QTL for 6 mph, while the majority of QTL for 18 mph were identified on two additional LGs, which may reveal a different genetic modulation during early and late muscle growth stages. Four potential candidate genes were identified from the QTL regions by homology searching of marker sequences against zebrafish genome. Hepcidin, a potential candidate gene identified from a QTL interval on LG16, was significantly associated with growth traits in the analyses of both phenotype-SNP association and mRNA expression between small-size and large-size groups of silver carp. These results provide a basis for elucidating the genetic mechanisms for growth and body formation in silver carp, a world aquaculture fish.

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Marker Development and Quantitative Trait Loci in a Fall-Sown Oat Recombinant Inbred Population

Crop Science ◽

10.2135/cropsci2010.04.0224 ◽

2011 ◽

Vol 51 (2) ◽

pp. 490-502 ◽

Cited By ~ 6

Author(s):

P. V. Maloney ◽

J. H. Lyerly ◽

D. R. Wooten ◽

J. M. Anderson ◽

D. P. Livingston ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Recombinant Inbred ◽

Marker Development ◽

Inbred Population ◽

Recombinant Inbred Population ◽

Trait Loci

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Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.)

Canadian Journal of Plant Science ◽

10.4141/cjps-2015-091 ◽

2015 ◽

Vol 95 (6) ◽

pp. 1133-1144

Author(s):

R. Khanal ◽

A. Navabi ◽

L. Lukens

Keyword(s):

Quantitative Trait Loci ◽

Qtl Mapping ◽

Linkage Map ◽

Inbred Line ◽

Recombinant Inbred Line ◽

Quantitative Trait ◽

Recombinant Inbred ◽

Map Construction ◽

Ril Population ◽

Trait Loci

Khanal, R., Navabi, A. and Lukens, L. 2015. Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.). Can. J. Plant Sci. 95: 1133–1144. Intermating of individuals in an F2 population increases genetic recombination between markers, which is useful for linkage map construction and quantitative trait loci (QTL) mapping. The objectives of this study were to compare the linkage maps and precision of QTL detection in an intermated recombinant inbred line (IRIL) population and a selfed recombinant inbred line (RIL) population. Both, IRIL and RIL, populations were developed from Zea mays inbred lines CG60 and CG102. The populations were grown in two environments to evaluate traits, and inbred lines from each population were genotyped with SSR and SNP markers for linkage map construction and QTL identification. In addition, we simulated RIL and IRIL populations from two inbred parents to compare the precision of QTL detection between simulated RIL and IRIL populations. In the empirical study, the linkage map was longer in RIL as compared with IRIL, and the average QTL support interval was reduced by 1.37-fold in the IRIL population compared with the RIL population. We detected 16 QTL for flowering time, plant height, leaf number, and stay green in at least one recombinant inbred line population. Two out of 16 QTL were shared between two recombinant inbred line populations. In the simulation study, the QTL support interval was reduced by 1.66-fold in the IRIL population as compared with the RIL population and linked QTL were identified more frequently in IRIL population as compared with RIL population. This study supports the utility of intermated RIL populations for precise QTL mapping.

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