Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits

Fan, Yapeng; Shabala, Sergey; Ma, Yanling; Xu, Ran; Zhou, Meixue

doi:10.1186/s12864-015-1243-8

Cited by 119 publications

(93 citation statements)

References 78 publications

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“…A recent study revealed that QTLs related to drought stress tolerances were placed on chromosome 2H and 5H (Fan et al 2015). The pivotal importance of the genomic regions for drought tolerance was also reported by Mehravaran et al (2014) on chromosomes 2H, 5H and 7H.…”

Section: Discussionmentioning

confidence: 99%

QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes

et al. 2016

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Drought has become more frequent in Central Europe causing large losses in cereal yields, especially of spring crops. The development of new varieties with increased tolerance to drought is a key tool for improvement of agricultural productivity. Material for the study consisted of 100 barley recombinant inbred lines (RILs) (LCam) derived from the cross between Syrian and European parents. The RILs and parental genotypes were examined in greenhouse experiments under well-watered and water-deficit conditions. During vegetation the date of heading, yield and yield-related traits were measured. RIL population was genotyped with microsatellite and single nucleotide polymorphism markers. This population, together with two other populations, was the basis for the consensus map construction, which was used for identification of quantitative trait loci (QTLs) affecting the traits. The studied lines showed a large variability in heading date. It was noted that drought-treatment negatively affected the yield and its components, especially when applied at the flag leaf stage. In total, 60 QTLs were detected on all the barley chromosomes. The largest number of QTLs was found on chromosome 2H. The main QTL associated with heading, located on chromosome 2H (Q.HD.LC-2H), was identified at SNP marker 5880–2547, in the vicinity of Ppd-H1 gene. SNP 5880–2547 was also the closest marker to QTLs associated with plant architecture, spike morphology and grain yield. The present study showed that the earliness allele from the Syrian parent, as introduced into the genome of an European variety could result in an improvement of barley yield performance under drought conditions.Electronic supplementary materialThe online version of this article (doi:10.1007/s13353-016-0363-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes

et al. 2016

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“…; Fan et al . ), and tissues in plants are often readily accessible from haploid life stages (e.g. Fins & Seeb ; Richier et al .…”

Section: Salmonids As Models For Studying Polyploid Vertebratesmentioning

confidence: 99%

Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing

Limborg

Seeb

2016

Molecular Ecology

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Many plants and animals of polyploid origin are currently enjoying a genomics explosion enabled by modern sequencing and genotyping technologies. However, routine filtering of duplicated loci in most studies using genotyping by sequencing introduces an unacceptable, but often overlooked, bias when detecting selection. Retained duplicates from ancient whole-genome duplications (WGDs) may be found throughout genomes, whereas retained duplicates from recent WGDs are concentrated at distal ends of some chromosome arms. Additionally, segmental duplicates can be found at distal ends or nearly anywhere in a genome. Evidence shows that these duplications facilitate adaptation through one of two pathways: neo-functionalization or increased gene expression. Filtering duplicates removes distal ends of some chromosomes, and distal ends are especially known to harbour adaptively important genes. Thus, filtering of duplicated loci impoverishes the interpretation of genomic data as signals from contiguous duplicated genes are ignored. We review existing strategies to genotype and map duplicated loci; we focus in detail on an overlooked strategy of using gynogenetic haploids (1N) as a part of new genotyping by sequencing studies. We provide guidelines on how to use this haploid strategy for studies on polyploid-origin vertebrates including how it can be used to screen duplicated loci in natural populations. We conclude by discussing areas of research that will benefit from better inclusion of polyploid loci; we particularly stress the sometimes overlooked fact that basing genomic studies on dense maps provides value added in the form of locating and annotating outlier loci or colocating outliers into islands of divergence.

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“…This approach has been successfully used to reveal the linkage between the correlated traits (Fan, Shabala, Ma, Xu, & Zhou, ; Gill et al, ; Ma et al, ; Wang et al, ). For examples, a new drought tolerant QTL was confirmed to have no significant effect on agronomic trait (Fan et al, ) and a significant contribution of membrane potential to both waterlogging and salinity tolerance was identified (Gill et al, ). In the present study, SIS revealed the closest correlation with SNaC and all the three QTL for SIS were located at similar positions to those for SNaC.…”

Section: Discussionmentioning

confidence: 99%

Identification of new QTL for salt tolerance from rice variety Pokkali

Chen

Yingguo

Chen

et al. 2020

J Agronomy Crop Science

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Salt stress is an ever‐present threat to rice production worldwide. Rice salinity tolerance is complex, both genetically and physiologically. The success and effectiveness in selecting salt‐tolerant rice variety require the identification of QTL for the tolerance and closely linked molecular markers. In the present study, a RIL population consisting of 148 lines, derived from a cross between IR29 (salt‐sensitive) and Pokkali (salt‐tolerant), was used to identify new QTL for salt tolerance and investigate the relationships between salt stress caused injury and the changes in different physiological and morphological traits at the seedling stage. 14,470 high‐quality SNP markers generated by the Rice 56K SNP array were converted to 1,467 bin markers for linkage mapping. A high‐density genetic linkage map covering 1,680.9 cM was constructed, with the physical to genetic distance ratio being 222 Kb/cM. In total, 23 QTL for different salt tolerance indices were identified, including the previously reported Saltol which is currently used in breeding programmes. Three QTL for salt injury score (SIS) were located on chromosomes 1, 4 and 12, all being closely related to the long‐distant Na+ transport from roots to shoots. These QTL showed additive effects, thus can be effectively used in breeding programme to pyramid various tolerance genes.

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Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits

Cited by 119 publications

References 78 publications

QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes

QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes

Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing

Identification of new QTL for salt tolerance from rice variety Pokkali

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