Posts Tagged ‘qtl’

Resistance of slow mildewing genes to stripe rust and leaf rust in common wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Acta Agronomica Sinica 40(9) : 1157-1564, 2014

Liu Jin-Dong; Chen Xin-Min; He Zhonghu; Wu Ling; Bai Bin; Li Zai-Feng; Xia Xian-Chun

Pyramiding quantitative trait loci (QTLs) is an effective method to improve resistance to powdery mildew, stripe rust, and leaf rust in common wheat. We have developed 21 lines (F6) carrying 2-5 slow mildewing QTLs by crossing slow powdery mildew cultivars Bainong 64 and Lumai 21 possessing four and three slow mildewing QTLs, respectively. These Flines were evaluated in the field in Pianxian, Sichuan and Tianshui, Gansu for stripe rust resistance and in Baoding, Hebei and Zhoukou, Henan for leaf rust resistance during the 2012-2013 cropping season. According to the maximum disease severities (MDS) and the area under the disease progress curve (AUDPC), QTLs QPm.caas-4DLQPm.caas-6BS and QPm.caas-2BL were highly resistant to stripe rust (P < 0.01), which explained 16.9%, 14.1%, and 17.3% of phenotypic variance, respectively. Locus QPm.caas-4DL also showed high resistance to leaf rust (P < 0.01) with phenotypic contribution of 35.3%. Lines that pyramided five (QPm.caas-1A/QPm.caas-4DLQPm.caas-2DL/QPm.caas-2BS/QPm.caas-2BL) and four (QPm.caas-1A/QPm.caas-4DL/QPm.caas-2BS/QPm.caas-2BL) QTLs exhibited higher resistance to both stripe and leaf rust compared with their parents. This result indicates that the combination of QPm.caas-4DL (from Bainong 64), QPm.caas-2BS and QPm.caas-2BL (Lumai 21) has a marked effect on improving adult resistance to powdery mildew, stripe rust and leaf rust, and the more QTLs are pyramided, the stronger slow disease resistance can be achieved. In breeding practice, the combination of 4-5 slow mildewing or rusting QTLs can result in durable resistance to multiple diseases.

Characterization of Yr54 and other genes associated with adult plant resistance to yellow rust and leaf rust in common wheat Quaiu 3

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2013

Basnet, B.R.; Singh, R.P.; Ibrahim, A.M.H.; Herrera-Foessel, S.A.; Huerta-Espino, J.; Lan, C.; Rudd, J.C.

Leaf rust (LR) and yellow rust (YR), caused by Puccinia triticina and Puccinia striiformis f. sp. tritici, respectively, are important diseases of wheat. Quaiu 3, a common wheat line developed at the International Maize and Wheat Improvement Center (CIMMYT), is immune to YR in Mexico despite seedling susceptibility to predominant races. Quaiu 3 also shows immunity to LR in field trials and is known to possess the race-specific gene Lr42. A mapping population of 182 recombinant inbred lines (RILs) was developed by crossing Quaiu 3 with susceptible Avocet-YrA and phenotyped with LR and YR in field trials for 2 years in Mexico. Quantitative trait loci (QTL) associated with YR and LR resistance in the RILs were identified using Diversity Arrays Technology and simple sequence repeat markers. A large-effect QTL on the long arm of chromosome 2D explained 49–54 % of the phenotypic variation in Quaiu 3 and was designated as Yr54. Two additional loci on 1BL and 3BS explained 8–17 % of the phenotypic variation for YR and coincided with previously characterized adult plant resistance (APR) genes Lr46/Yr29 and Sr2/Yr30, respectively. QTL on 1DS and 1BL corresponding to Lr42 and Lr46/Yr29, respectively, contributed 60–71 % of the variation for LR resistance. A locus on 3D associated with APR to both diseases explained up to 7 % of the phenotypic variance. Additional Avocet-YrA-derived minor QTL were also detected for YR on chromosomes 1A, 3D, 4A, and 6A. Yr54 is a newly characterized APR gene which can be combined with other genes by using closely linked molecular markers.

The growths of leaves, shoots, roots and reproductive organs partly share their genetic control in maize plants

Posted by Carelia Juarez on , in Journal Articles

Published in Plant, Cell and Environment 36 (6) : 1105-1119, 2013

G. Dignat, C. Welcker, M. Sawlins, J.M. Ribaut and F. Tardieu

We have tested to what extent the growth ability of several organs of maize share a common genetic control. Every night, leaf elongation rate reaches a maximum value (LERmax) that has a high heritability, is repeatable between experiments and is correlated with final leaf length. Firstly, we summarized quantitative trait loci (QTLs) of LERmax and of leaf length in three mapping populations. Among the 14 consensus QTLs (cQTLs) of leaf length, seven co-located with cQTLs of LERmax with consistent allelic effects. Nine cQTLs of LERmax(4% of the genome) were highly reliable and confirmed by introgression lines. We then compared these QTLs with those affecting the growths of leaves, shoots, roots or young reproductive organs, detected with the same mapping populations in three field experiments or in literature datasets. Five of the nine most reliable cQTLs of LERmax co-located with QTLs involved in the growth of other organs (but not in flowering time) with consistent allelic effects. Reciprocally, two-thirds of the 20 QTLs of growth of different organs co-located with cQTLs of LERmax. Hence, LERmax, as determined in a phenotyping platform, is an indicator of the growth ability of other organs of the plant in controlled or in-field conditions.


Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2012

A. Singh, M. P. Pandey, A. K. Singh, R. E. Knox, K. Ammar, J. M. Clarke, F. R. Clarke, R. P. Singh, C. J. Pozniak, R. M. DePauw, B. D. McCallum, R. D. Cuthbert, H. S. Randhawa and T. G. Fetch Jr.

Leaf rust (Puccinia triticina Eriks.), stripe rust (Puccinia striiformis f. tritici Eriks.) and stem rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, stripe and stem rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf rust races BBG/BN and BBG/BP and adult plant response was determined in three field rust nurseries near El Batan, Obregon and Toluca, Mexico. Stripe rust response was recorded in 2009 and 2011 nurseries near Toluca and near Njoro, Kenya in 2010. Response to stem rust was recorded in field nurseries near Njoro, Kenya, in 2010 and 2011. Sachem was resistant to leaf, stripe and stem rust. A major leaf rust quantitative trait locus (QTL) was identified on chromosome 7B at Xgwm146 in Sachem. In the same region on 7B, a stripe rust QTL was identified in Strongfield. Leaf and stripe rust QTL around DArT marker wPt3451 were identified on chromosome 1B. On chromosome 2B, a significant leaf rust QTL was detected conferred by Strongfield, and at the same QTL, a Yr gene derived from Sachem conferred resistance. Significant stem rust resistance QTL were detected on chromosome 4B. Consistent interactions among loci for resistance to each rust type across nurseries were detected, especially for leaf rust QTL on 7B. Sachem and Strongfield offer useful sources of rust resistance genes for durum rust breeding.


Multi-trait and multi-environment QTL analyses for resistance to wheat diseases

Posted by Carelia Juarez on , in Journal Articles

Published in PLoS ONE 7 (6): e38008, 2012

Sukhwinder-Singh, Mateo V. Hernandez, Jose Crossa, Pawan K. Singh, Navtej S. Bains, Kuldeep Singh, Indu Sharma


Stripe rust, leaf rust, tan spot, and Karnal bunt are economically significant diseases impacting wheat production. The objectives of this study were to identify quantitative trait loci for resistance to these diseases in a recombinant inbred line (RIL) from a cross HD29/WH542, and to evaluate the evidence for the presence loci on chromosome region conferring multiple disease resistance.

Methodology/Principal Findings

The RIL population was evaluated for four diseases and genotyped with DNA markers. Multi-trait (MT) analysis revealed thirteen QTLs on nine chromosomes, significantly associated with resistance. Phenotypic variation explained by all significant QTLs for KB, TS, Yr, Lr diseases were 57%, 55%, 38% and 22%, respectively. Marginal trait analysis identified the most significant QTLs for resistance to KB on chromosomes 1BS, 2DS, 3BS, 4BL, 5BL, and 5DL. Chromosomes 3AS and 4BL showed significant association with TS resistance. Significant QTLs for Yr resistance were identified on chromosomes 2AS, 4BL and 5BL, while Lr was significant on 6DS. MT analysis revealed that all the QTLs except 3BL significantly reduce KB and was contributed from parent HD29 while all resistant QTLs for TS except on chromosomes 2DS.1, 2DS.2 and 3BL came from WH542. Five resistant QTLs for Yr and six for Lr were contributed from parents WH542 and HD29 respectively. Chromosome region on 4BL showed significant association to KB, TS, and Yr in the population. The multi environment analysis for KB identified three putative QTLs of which two new QTLs, mapped on chromosomes 3BS and 5DL explained 10 and 20% of the phenotypic variation, respectively.


This study revealed that MT analysis is an effective tool for detection of multi-trait QTLs for disease resistance. This approach is a more effective and practical than individual QTL mapping analyses. MT analysis identified RILs that combine resistance to multiple diseases from parents WH542 and/or HD29.

Genomic characterization of drought tolerance-related traits in spring wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Euphytica 186 (1): 265-276, 2012

Sundeep Kumar, Sunish Kumar Sehgal, Uttam Kumar, P. V. Vara Prasad, Arun Kumar Joshi and Bikram Singh Gill

Drought tolerance was investigated in ‘C306’, one of the most drought tolerant wheat cultivars bred in India in the 1960’s. An intervarietal mapping population of recombinant inbred lines of the cross ‘C306’ × ‘HUW206’ was evaluated for drought tolerance components, namely potential quantum efficiency of photosystem (PS) II (Fv/Fm), chlorophyll content (Chl), flag leaf temperature (Lt), and grain yield per plant (Gyp) under stress. Three independent experiments were conducted under well-watered and water-stressed conditions in greenhouses and growth chambers at Kansas State University (USA). Five hundred and sixty microsatellite markers covering the entire genome were screened for polymorphism between the parents. A QTL (QLt.ksu-1D) for Lt (low flag leaf temperature under stress) on the short arm of chromosome 1D between markers Xbarc271 and Xgwm337 at LOD 3.5 explained 37% of the phenotypic variation. A QTL for Fv/Fm (QF v /F m .ksu-3B) and Chl (QChl.ksu-3B) controlling quantum efficiency of PS II and chlorophyll content under stress were co-localized on chromosome 3B in the marker interval Xbarc68-Xbarc101 and explained 35-40% of the phenotypic variation for each trait. A QTL (QGyp.ksu-4A) for Gyp on chromosome 4A at a LOD value of 3.2 explained 16.3% of the phenotypic variation. Inconsistent QTLs were observed for Fv/Fm on chromosomes 3A, 6A, 2B, 4B, and 4D; for Chl on 3A, 6A, 2B and 4B; and for Lt on 1A, 3A 6A, 3B and 5B. The identified QTLs give a first glimpse of the genetics of drought tolerance in C306 and need to be validated in field experiments using the marker-phenotype linkages reported here.

Characterization of a cell wall invertase gene TaCwi-A1 on common wheat chromosome 2A and development of functional markers

Posted by on , in Journal Articles

Published in Molecular Breeding 29(1): 43-52, 2012

Dongyun Ma, Jun Yan, Zhonghu He, Ling Wu and Xianchun Xia

Cell wall invertase (CWI) is a critical enzyme for sink tissue development and carbon partition, and has a high association with kernel weight. Characterization of Cwi genes and development of functional markers are of importance for marker-assisted selection in wheat breeding. In the present study, the full-length genomic DNA sequence of a Cwi gene located on wheat chromosome 2A, designated TaCwiA1, was characterized by in silico cloning and experimental validation. TaCwiA1 comprises seven exons and six introns, with 3,676 bp in total, and an open reading frame (ORF) of 1,767 bp. A pair of complementary dominant markers, CWI21 and CWI22, was developed based on allelic variations at the TaCwiA1 locus. A 404-bp PCR fragment was amplified by CWI21 in varieties with lower kernel weights, whereas a 402-bp fragment was generated by CWI22 in the varieties with higher kernel weights. The markers CWI21 and CWI22 were located on chromosome 2AL using a F2:3 population from a cross Doumai/Shi 4185, and a set of Chinese Spring nullisomic–tetrasomic lines. They were linked to the SSR locus Xbarc152AL with a genetic distance of 10.9 cM. QTL analysis indicated that TaCwiA1 could explain 4.8% of phenotypic variance for kernel weight over 2 years. Two sets of Chinese landraces and two sets of commercial wheat varieties were used to validate the association of CWI21 and CWI22 with kernel weight. The results indicated that the functional markers CWI21 and CWI22 were closely related to kernel weight and could be used in wheat breeding for improving grain yield.

New Book in the Library: A guide to QTL Mapping with R/qtl

Posted by Jose Juan Caballero on , in New Acquisitions

ISBN: 978-0387921242

Karl W. Broman

Saunak Sen

A Guide to QTL Mapping with R/qtl 

Quantitative trait locus (QTL) mapping is used to discover the genetic and molecular architecture underlying complex quantitative traits. It has important applications in agricultural, evolutionary, and biomedical research. R/qtl is an extensible, interactive environment for QTL mapping in experimental crosses. It is implemented as a package for the widely used open source statistical software R and contains a diverse array of QTL mapping methods, diagnostic tools for ensuring high-quality data, and facilities for the fit and exploration of multiple-QTL models, including QTL x QTL and QTL x environment interactions. This book is a comprehensive guide to the practice of QTL mapping and the use of R/qtl, including study design, data import and simulation, data diagnostics, interval mapping and generalizations, two-dimensional genome scans, and the consideration of complex multiple-QTL models. Two moderately challenging case studies illustrate QTL analysis in its entirety.

The book alternates between QTL mapping theory and examples illustrating the use of R/qtl. Novice readers will find detailed explanations of the important statistical concepts and, through the extensive software illustrations, will be able to apply these concepts in their own research. Experienced readers will find details on the underlying algorithms and the implementation of extensions to R/qtl. There are 150 figures, including 90 in full color.

Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2 population

Posted by on , in Journal Articles

Published in Theoretical and Applied Genetics 120(2):333-340, 2010

Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2 population.

Jihua Tang, Jianbing Yan, Xiqing Ma, Wentao Teng, Weiren Wu, Jingrui Dai, Baldev S. Dhillon, Albrecht E. Melchinger and Jiansheng Li 

The genetic basis of heterosis for grain yield and its components was investigated at the single- and two-locus levels using molecular markers with an immortalized F2 (IF2) population, which was developed by pair crosses among recombinant inbred lines (RILs) derived from the elite maize hybrid Yuyu22. Mid-parent heterosis of each cross in the IF2 population was used to map heterotic quantitative trait loci. A total of 13 heterotic loci (HL) were detected. These included three HL for grain yield, seven for ear length, one for ear row number and two for 100-kernel weight. A total of 143 digenic interactions contributing to mid-parent heterosis were detected at the two-locus level involving all three types of interactions (additive × additive = AA, additive × dominance = AD or DA, dominance × dominance = DD). There were 25 digenic interactions for grain yield, 36 for ear length, 31 for ear row number and 51 for 100-kernel weight. Altogether, dominance effects of HL at the single-locus level as well as AA interactions played an important role in the genetic basis of heterosis for grain yield and its components in Yuyu22.

Characterization of the effect of a QTL for drought resistance in rice, qtl12.1 , over a range of environments in the Philippines and eastern India

Posted by on , in Journal Articles

Published in Euphytica 166(2): 207-217

Characterization of the effect of a QTL for drought resistance in rice, qtl12.1 , over a range of environments in the Philippines and eastern India

Jérôme Bernier, Arvind Kumar, Ramaiah Venuprasad, Dean Spaner, Satish Verulkar, Nimai P. Mandal, Pramod K. Sinha, Puvvada Peeraju, Praba R. Dongre, R. N. Mahto and Gary Atlin

A large-effect QTL for grain yield under drought conditions (qtl12.1) was reported in a rice mapping population derived from Vandana and Way Rarem. Here, we measured the effect of qtl12.1 on grain yield and associated traits in 21 field trials: ten at IRRI in the Philippines and 11 in the target environment of eastern India. The relative effect of the QTL on grain yield increased with increasing intensity of drought stress, from having no effect under well-watered conditions to having an additive effect of more than 40% of the trial mean in the most severe stress treatments. The QTL improved grain yield in nine out of ten direct-seeded upland trials where drought stress was severe or moderate, but no effect was measured under well-watered aerobic conditions or under transplanted lowland conditions. These trials confirm that qtl12.1 has a large and consistent effect on grain yield under upland drought stress conditions, in a wide range of environments