Dissecting the genetic architecture of waterlogging stress-related traits uncovers a key waterlogging tolerance gene in maize

Key message

A key candidate gene, GRMZM2G110141, which could be used in marker-assisted selection in maize breeding programs, was detected among the 16 genetic loci associated with waterlogging tolerance identified through genome-wide association study.

Abstract

Waterlogging stress seriously affects the growth and development of upland crops such as maize (Zea mays L.). However, the genetic basis of waterlogging tolerance in crop plants is largely unknown. Here, we identified genetic loci for waterlogging tolerance-related traits by conducting a genome-wide association study using maize phenotypes evaluated in the greenhouse under waterlogging stress and normal conditions. A total of 110 trait-single nucleotide polymorphism associations spanning 16 genomic regions were identified; single associations explained 2.88–10.67% of the phenotypic variance. Among the genomic regions identified, 14 co-localized with previously detected waterlogging tolerance-related quantitative trail loci. Furthermore, 33 candidate genes involved in a wide range of stress-response pathways were predicted. We resequenced a key candidate gene (GRMZM2G110141) in 138 randomly selected inbred lines and found that variations in the 5?-UTR and in the mRNA abundance of this gene under waterlogging conditions were significantly associated with leaf injury. Furthermore, we detected favorable alleles of this gene and validated the favorable alleles in two different recombinant inbred line populations. These alleles enhanced waterlogging tolerance in segregating populations, strongly suggesting that GRMZM2G110141 is a key waterlogging tolerance gene. The set of waterlogging tolerance-related genomic regions and associated markers identified here could be valuable for isolating waterlogging tolerance genes and improving this trait in maize.

     

Tolerance to ion toxicities enhances wheat (Triticum aestivum L.) grain yield in waterlogged acidic soils

Aims

The high concentrations of Mn, Fe and Al in acid soils during waterlogging impair root and shoot growth more severely in intolerant than tolerant wheat genotypes. This study aims to establish whether this difference in vegetative growth and survival during waterlogging (1) is verifiable across a range of tolerant/intolerant genotypes and acid soils, and (2) results in improved recovery after cessation of waterlogging and enhanced grain yield.

Methods

Wheat genotypes contrasting in their tolerance to ion toxicities were grown in four acid soils until 63DAS and maturity, with a 42-day waterlogging treatment imposed at 21 DAS.

Results

The shoot Al, Mn and Fe concentrations increased by up to 5-, 3- and 9-fold respectively due to waterlogging in various soils. Compared to the intolerant lines, Al-, Mn- and Fe-tolerant genotypes maintained a relatively lower increase in shoot concentrations of Al (79 vs. 117%), Mn (90 vs. 101%) and Fe (171 vs. 252%) and demonstrated better waterlogging tolerance at the vegetative stage expressed in relative root (38% vs. 25%) and shoot (62% vs. 52%) growth. After cessation of waterlogging and the continued growth to maturity, tolerant genotypes maintained a relatively lower plant concentration of Al, Mn and Fe, but produced a higher above-ground biomass (74% vs. 56%) and most importantly demonstrated improved waterlogging tolerance (a relative grain yield of 78% vs. 54%) compared to intolerant genotypes. Maturity following waterlogging stress was delayed less in tolerant than intolerant genotypes (114 vs. 124%, respectively), which would reduce the potential yield loss where post-anthesis coincides with drought.

Conclusions

The results confirm the validity of a novel approach of enhancing waterlogging tolerance of wheat genotypes grown in acid soil via increased tolerance to ion toxicities.     

Identifying the critical period for waterlogging on yield and its components in wheat and barley

Background and aims

Crop tolerance to waterlogging depends on factors such as species sensitivity and the stage of development that waterlogging occurs. The aim of this study was to identify the critical period for waterlogging on grain yield and its components, when applied during different stages of crop development in wheat and barley.

Methods

Two experiments were carried out (E1: early sowing date, under greenhouse; E2: late sowing date, under natural conditions). Waterlogging was imposed during 15–20 days in 5 consecutive periods during the crop cycle (from Leaf 1 emergence to maturity).

Results

The greatest yield penalties occurred when waterlogging was applied from Leaf 7 appearance on the main stem to anthesis (from 34 to 92 % of losses in wheat, and from 40 to 79 % in barley for E1 and E2 respectively). Waterlogging during grain filling reduced yield to a lesser degree. In wheat, reductions in grain number were mostly explained by reduced grain number per spike while in barley, by variations in the number of spikes per plant.

Conclusions

The time around anthesis was identified as the most susceptible period to waterlogging in wheat and barley. Exposing the crop to more stressful conditions, e.g. delaying sowing date, magnified the negative responses to waterlogging, although the most sensitive stage (around anthesis) remained unchanged.     

A Single Locus Is Responsible for Salinity Tolerance in a Chinese Landrace Barley (Hordeum vulgare L.)

Introduction

Salinity and waterlogging are two major abiotic stresses severely limiting barley production. The lack of a reliable screening method makes it very hard to improve the tolerance through breeding programs.

Methods

This work used 188 DH lines from a cross between a Chinese landrace variety, TX9425 (waterlogging and salinity tolerant), and a Japanese malting barley, Naso Nijo (waterlogging and salinity sensitive), to identify QTLs associated with the tolerance.

Results

Four QTLs were found for waterlogging tolerance. The salinity tolerance was evaluated with both a hydroponic system and in potting mixture. In the trial with potting mixture, only one major QTL was identified to associate with salinity tolerance. This QTL explained nearly 50% of the phenotypic variation, which makes it possible for further fine mapping and cloning of the gene. This QTL was also identified in the hydroponic experiment for different salt-related traits. The position of this QTL was located at a similar position to one of the major QTLs for waterlogging tolerance, indicating the possibility of similar mechanisms controlling both waterlogging and salinity tolerance.

Conclusion

The markers associated with the QTL provided a unique opportunity in breeding programs for selection of salinity and waterlogging tolerance.     

Review of wheat improvement for waterlogging tolerance in Australia and India: the importance of anaerobiosis and element toxicities associated with different soils

Background and Aims

The lack of knowledge about key traits in field environments is a major constraint to germplasm improvement and crop management because waterlogging-prone environments are highly diverse and complex, and the mechanisms of tolerance to waterlogging include a large range of traits. A model is proposed that waterlogging tolerance is a product of tolerance to anaerobiosis and high microelement concentrations. This is further evaluated with the aim of prioritizing traits required for waterlogging tolerance of wheat in the field.

Methods

Waterlogging tolerance mechanisms of wheat are evaluated in a range of diverse environments through a review of past research in Australia and India; this includes selected soils and plant data, including plant growth under waterlogged and drained conditions in different environments. Measurements focus on changes in redox potential and concentrations of diverse elements in soils and plants during waterlogging.

Key Results

(a) Waterlogging tolerance of wheat in one location often does not relate to another, and (b) element toxicities are often a major constraint in waterlogged environments. Important element toxicities in different soils during waterlogging include Mn, Fe, Na, Al and B. This is the first time that Al and B toxicities have been indicated for wheat in waterlogged soils in India. These results support and extend the well-known interactions of salinity/Na and waterlogging/hypoxia tolerance.

Conclusions

Diverse element toxicities (or deficiencies) that are exacerbated during waterlogging are proposed as a major reason why waterlogging tolerance at one site is often not replicated at another. Recommendations for germplasm improvement for waterlogging tolerance include use of inductively coupled plasma analyses of soils and plants.Key words: Waterlogging, microelements, toxicity, redox potential, wheat, anaerobiosis

‘No grain is ever produced without water, but too much water tends to spoil the grain and inundation is as injurious to growth as dearth of water.’ Narada Smriti XI, 19; circa 3000 bc.‘Waterlogging’ is defined as a condition of the soil where excess water limits gas diffusion; while ‘waterlogging tolerance’ is defined as survival or the maintenance of high growth rates, biomass accumulation or grain yield under waterlogging relative to non waterlogged (usually drained soil) conditions (Setter and Waters, 2003).

     

Efficacy of SSH PCR in isolating differentially expressed genes

Background  

Suppression Subtractive Hybridization PCR (SSH PCR) is a sophisticated cDNA subtraction method to enrich and isolate differentially expressed genes. Despite its popularity, the method has not been thoroughly studied for its practical efficacy and potential limitations.     

Construction and analysis of cotton (<Emphasis Type="Italic">Gossypium arboreum</Emphasis>L.) drought-related cDNA library

Background

Drought is one of the most important environmental factors causing water stress for cotton, and it greatly limits cotton growth and crop productivity. So far only a few drought-tolerance genes have been functionally characterized in details, and most efforts on this topic have been made in model organisms. Therefore, to identify more drought-related genes in cotton plays a crucial role in elucidating the underlying mechanisms of drought tolerance as well as utilizing bioengineering techniques to improve the tolerance in this organism.

Findings

Here we constructed a subtractive drought-tolerance cDNA library using suppressive subtractive hybridization (SSH). Through differential screening and bioinformatics analysis, we identified 392 positive clones with differential expression, corresponding 265 unique genes. By BLAST search against Genbank, we found that more than half of these EST sequences were homologous to those previously known drought-related genes and that there were 57 sequences with unknown functions, suggesting that many more genes are involved in this complex trait. Moreover, using RT-PCR, we examined the expression of nine representative candidate genes and confirmed that their expression levels were increased at different levels under drought stress.

Conclusion

Our results show that drought tolerance is a complex trait in cotton, which involves the coordination of many genes and multiple metabolism pathways. The candidate EST sequences we identified here would facilitate further functional studies of drought-related genes and provide important insights into the molecular mechanisms of drought-stress tolerance and genetic breeding in cotton.

     

Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns

Waterlogging is a common adverse environmental condition that limits plant growth. Sesame (Sesamum indicum) is considered a drought-tolerant oil crop but is typically susceptible to harmful effects from waterlogging. The present study used comparative analysis to explore the waterlogging stress response associated with two sesame genotypes. The RNA-seq dataset generated during a time course of 0, 3, 9 and 15 h of waterlogging as well as 20 h post-drainage indicated that stress gradually suppressed the expression of sesame genes, with 9 h as the critical time point for the response of sesame to waterlogging stress. Of the 19,316 genes expressed during waterlogging, 72.1% were affected significantly. Sesame of both tolerant and susceptible genotypes showed decreased numbers of upregulated differentially expressed genes (DEGs) but increased numbers of downregulated DEGs at the onset of waterlogging. However, the tolerant-genotype sesame exhibited 25.5% more upregulated DEGs and 29.7% fewer downregulated DEGs than those of the susceptible-genotype strain between 3 and 15 h. The results indicated that the tolerant sesame displayed a more positive gene response to waterlogging. A total of 1,379 genes were significantly induced and commonly expressed in sesame under waterlogging conditions from 3 to 15 h regardless of tolerance level; of these genes, 98 are known homologous stress responsive genes, while the remaining 1,281 are newly reported here. This gene set may represent the core genes that function in response to waterlogging, including those related mainly to energy metabolism and phenylpropanoid biosynthesis. Furthermore, a set of 3,016 genes functioning in energy supply and cell repair or formation was activated in sesame recovery from waterlogging stress. A comparative analysis between sesame of the tolerant and susceptible genotypes revealed 66 genes that may be candidates for improving sesame tolerance to waterlogging. This study provided a comprehensive picture of the sesame gene expression pattern in response to waterlogging stress. These results will help dissect the mechanism of the sesame response to waterlogging and identify candidate genes to improve its tolerance.     

Identification of genes differentially expressed during larval molting and metamorphosis of <Emphasis Type="Italic">Helicoverpa armigera</Emphasis>

Background  

Larval molting and metamorphosis are important physiological processes in the life cycle of the holometabolous insect. We used suppression subtractive hybridization (SSH) to identify genes differentially expressed during larval molting and metamorphosis.