Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

Xu, Jie; Yuan, Yibing; Xu, Yunbi; Zhang, Gengyun; Guo, Xiaosen; Wu, Fengkai; Wang, Qi; Tang, Rong; Pan, Guangtang; Cao, Mengji; Tang, Qilin; Gao, Shibin; Liu, Yaxi; Wang, Jing; Long, Hai; Lu, Yanli

doi:10.1186/1471-2229-14-83

Cited by 100 publications

(86 citation statements)

References 78 publications

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“…Transcriptome analysis of the wild rice Oryza rufipogon has led to the identification of 37 drought response genes differentially expressed in roots on application of drought stress (Tian et al, 2015). A transcription factor HYR which is associated with photosynthetic carbon metabolism has been identified, and its expression in rice has led to enhanced photosynthesis under drought and other environmental stresses, and resulted in increased yield under stress (Ambavaram et al, 2014 (Xu et al, 2014). Similar approaches in rice can be used to identify candidate genes responsible for drought tolerance, subsequently to be used in crop improvement programmes.…”

Section: Prospects For Increasing Drought Tolerance In Ricementioning

confidence: 99%

Morphophysiological and molecular effects of drought stress in rice

et al. 2016

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Drought is a major abiotic stress that adversely affects the rice growth, mostly in the rainfed ecosystem that ultimately affects the biomass production and yield. Rice needs to adapt a series of physiological mechanisms with complicated regulatory network to fight and cope up with the unfavourable conditions due to drought stress. Morphological and physiological response in rice include inhibition of seed germination, slower growth rate, low root and shoot length, lower chlorophyll content, stomatal closure, lower rate of photosynthesis, yield reduction etc. Stress condition further results in development of response at the molecular level by the generation of reactive oxygen species (ROS) such as O2*-, H2O2, 1O2, OH* etc. which incites oxidative stress in the plants. Oxidative stress is overcome by the inherent capacity of plants to produce antioxidant species which may be enzymatic or non-enzymatic in nature. If however antioxidant defence mechanism cannot overpower the ROS generated, they cause oxidative damage to the plant tissues such as lipid peroxidation, protein oxidation, DNA damage, etc. resulting in cell death. Unlike other stresses, drought affects the physiology and biochemistry of the rice which adversely affects in the morphology and consequently delimits the yield of the plant. Therefore, understanding the morphological, biochemical and molecular mechanisms involved in rice against drought is utmost necessary for rice breeders to improve the rice for drought tolerant/resistance varieties for future green revolution. In this review, an attempt has been made to highlight the complex regulatory network involved in rice against drought with special emphasis on morphological, physiological and molecular mechanisms and to discuss the prospective and challenges for future plant breeders.

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Section: Prospects For Increasing Drought Tolerance In Ricementioning

confidence: 99%

Morphophysiological and molecular effects of drought stress in rice

et al. 2016

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“…In recent years, molecular mechanisms for tolerance to drought stress in plants have become an active area of investigation and many genes regulated by drought stress have been reported in a variety of plants (Sehgal et al, 2012;Thudi et al, 2014;Xu et al, 2014). Very little is known about the physiological and molecular mechanisms by which the model legume M. truncatula responds to drought stress.…”

Section: Introductionmentioning

confidence: 99%

Morph-physiological responses to water deficit in parental genotypes of Medicago truncatula recombinant inbred lines

Mahfoudh¹,

Abdelly²

2016

Afr. J. Biotechnol.

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Medicago truncatula is an omni-Mediterranean species grown as an annual forage legume. In addition to its small genome size and simple genetics, M. truncatula harbors several attributes which make it an attractive model legume. In this study, we investigated morphological and photosynthetic responses to water deficit in parental genotypes of M. truncatula recombinant inbred lines. Ten parental lines were cultivated under three water regimes (100% of field capacity (FC), 50% FC and 30% FC) and were harvested at flowering time and at the end of their lifecycle. Results from ANOVA showed that variability of measured parameters was explained by the effects of line, treatment and their interaction with treatment factor recorded the highest values. Out of the 27 traits, 14 were influenced by the line x treatment interaction. High to moderate broad-sense heritability (H²) were observed for most of the traits under control treatment and drought stress. Most of the correlations between measured traits were positive under the three water regimes. The flowering time was positively correlated with aerial and root growth rate. The tolerance of lines to water deficit seems to depend, in particular, on their ability to maintain higher photosynthetic activity. In 30% FC, principal component analysis clustered lines into two groups. The Jemalong A17 line was the least affected for most phenotypic parameters. Hence, all populations of recombinant inbred lines derived from crosses between Jemalong A17 and the remaining lines were useful for the identification of the genetic determinants for tolerance to water deficit in M. truncatula.

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“…Chen et al (2014) have identified more than 10,000,000 SNP loci from 801 re-sequenced rice varieties. Xu et al (2014) have found a total of 6,385,011 SNPs through re-sequencing 15 maize inbreds and compared them to maize B73 reference genome. Another study yielded a total of 4,290,679 unique SNPs from eight tomato lines when each genome was separately compared to the reference genome (Causse et al 2013).…”

Section: Molecular Marker Discoverymentioning

confidence: 99%

“…Loss of this gene (DST) function will enhance stomatal closure and decrease stomatal density, resulting in improved drought and salt tolerance in rice (Huang et al 2009b). Similarly, after the genome sequence of maize became available, candidate genes were identified for drought tolerance so that they could be used for the development of drought tolerance varieties (Xu et al 2014). In one study, more than 6,000 SNPs were found in drought stress related genes from two contrasting cultivars of Soybean: sensitive (BR 16) and tolerant (Embrapa 48).…”

Section: Abiotic and Biotic Stress Tolerance Variety Developmentmentioning

confidence: 99%

“…Analysis of DNA sequence variations in candidate genes based on morphological phenotypes is a good way to identify causal genes for these traits. Many studies have reported genome-wide evaluations for different breeding varieties or lines of plants with strong genetic diversity across different chromosomal regions in association with different phenotypic changes (Lam et al 2010;Riedelsheimer et al 2012;Causse et al 2013;Chen et al 2014;Xu et al 2014).…”

Section: Introductionmentioning

confidence: 99%

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Genome Sequencing, a Milestone for Genomic Research and Plant Breeding

Huq¹,

Akter²,

Jung³

et al. 2016

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Plant Breed. Biotech. 2016 (February) ABSTRACT Plant breeding programs are often used to improve varieties through creating diverse agronomic traits. During a breeding program, a lot of genetic diversities are created in the genome after different generations through homologous recombination. Genome sequencing technology has revolutionized the discovery of genes and molecular markers associated with diverse agronomic traits in crop improvement programs. Genomic research is now in the peak of success, thus creating new opportunities for crop improvement modern sequencing technology is now capable of sequencing thousands to millions of bases per run. Modern sequencing technologies enable the sequencing of different cultivars with small to complex genomes at a reasonable time and cost. These massive data can be used to identify important agronomic traits of crops such as fruit color, size, ripening, flowering time adaptation, grain yield, and quality maintenance. In addition, they can be used to develop crop varieties. This mini-review is focused on the role of genome sequencing in genomic research and plant breeding for crop improvements.

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Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

Cited by 100 publications

References 78 publications

Morphophysiological and molecular effects of drought stress in rice

Morphophysiological and molecular effects of drought stress in rice

Morph-physiological responses to water deficit in parental genotypes of Medicago truncatula recombinant inbred lines

Genome Sequencing, a Milestone for Genomic Research and Plant Breeding

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