Identification of loci contributing to maize drought tolerance in a genome-wide association study

Wang, Nan; Wang, Zhenping; Liang, Xiaoling; Weng, Jianfeng; Lv, Xiangling; Zhang, Degui; Yang, Jie; Yong, Hongjun; Li, Mingshun; Jiang, L Y; Zhang, Shihuang; Zhang, Hao; Li, Xinhai

doi:10.1007/s10681-016-1688-0

Cited by 19 publications

(14 citation statements)

References 61 publications

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“…The positive significant associations were observed among traits suggested that these traits might share some common genomic regions. Similar significant relationships for agronomic traits under normal and stress conditions were reported in previous studies [ 26 , 28 , 41 ]. Moderate to strong negative correlations was observed between ASI and other traits (PH, EH, EPO, GY) under both normal and heat stress conditions.…”

Section: Discussionsupporting

confidence: 88%

“…It has been postulated that genes associated with the target traits significantly could be resequenced from contrasting lines to identify favorable alleles for trait improvement and SNP/InDELs could be potentially converted to simple PCR-based markers to follow MAS in molecular breeding [ 44 , 45 ]. Several studies have been made in maize for identification of associated SNPs with a particular trait using GWAS analysis [ 25 , 26 , 30 , 41 ]. We identified 130 SNPs associated with different traits distributed over all the 10 maize chromosomes but most of them localized on chromosomes 3, 8 and 10 under normal conditions.…”

Section: Discussionmentioning

confidence: 99%

“…One of the genes GRMZM2G125777 that encodes NAC domain containing protein 2, a transcription factor expressed in different tissues, was strongly associated with ear relative position, hundred kernel weights and timing of male and female flowering [ 26 ]. Similarly, Wang et al [ 41 ] identified 206 significant SNPs associated with 115 candidate genes for drought tolerance and related traits. Zaidi et al [ 28 ] revealed 67 significantly associated SNPs for root structural traits whereas Frey et al [ 46 ] revealed 607 heat responsive genes as well as 39 heat tolerance genes.…”

Section: Discussionmentioning

confidence: 99%

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Genome wide association mapping for heat tolerance in sub-tropical maize

et al. 2021

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Background Heat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program. Results An association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology. Conclusions The present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome wide association mapping for heat tolerance in sub-tropical maize

et al. 2021

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“…Fe and Zn toxicity tolerance processes are difficult to define and measure. The secondary traits or symptoms associated with stress can help breeders make perform selection for stress tolerance [ 49 ]. In this study, SH, SFW and SDW were easily measured and more reliable than RL, RDW and SWC.…”

Section: Discussionmentioning

confidence: 99%

QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

et al. 2017

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BackgroundFerrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity and greatly affect rice yield and quality. To improve rice production, understanding the genetic and molecular resistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is an effective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the genetic relationship between them in a genetically diverse population.ResultsA total of 29 and 31 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW), shoot water content (SWC) and shoot ion concentrations (SFe or SZn) were identified at seedling stage in Fe and Zn experiments, respectively. Five toxicity tolerance QTL (qSdw3a, qSdw3b, qSdw12 and qSFe5 / qSZn5) were detected in the same genomic regions under the two stress conditions and 22 candidate genes for 10 important QTL regions were also determined by haplotype analyses.ConclusionRice plants share partial genetic overlaps of Fe and Zn toxicity tolerance at seedling stage. Candidate genes putatively affecting Fe and Zn toxicity tolerance identified in this study provide valuable information for future functional characterization and improvement of rice tolerance to Fe and Zn toxicity by marker-assisted selection or designed QTL pyramiding.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4221-5) contains supplementary material, which is available to authorized users.

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“…GWAS is fast becoming a standard tool for establishing marker trait associations. Regarding drought tolerance it has been performed in various crops like rice (WU et al, 2015), wheat (EDAE et al, 2014), maize (LIU et al, 2013;XUE et al, 2013;WANG et al, 2016) and chick pea (THUDI et al, 2014). Regarding soybean, DHANAPAL et al, (2015) using GWAS identified 21 putative loci for carbon isotope ratio as a surrogate trait of water use efficiency (WUE).…”

Section: Association Mapping (Am) and Genome Wide Association Studiesmentioning

confidence: 99%

Achievements and prospects of molecular breeding for drought tolerance in soybean [Glycine max (L.) merr.]

Alam¹

2018

Genetika

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Drought stress is one of the most serious constraints of soybean production worldwide. While the drought tolerance is one of the most complex attributes for soybean breeders to deal with. Due to complex (quantitative) nature of drought tolerance trait, the progress to develop drought tolerant plants is slow. Molecular breeding thus emerged as a necessary approach in soybean breeding programs. A plethora of genetic information regarding the functional genomics and other molecular resources is available. The effective and astute use of these resources will certainly facilitate the breeders to develop soybean cultivars tolerant to drought.

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Identification of loci contributing to maize drought tolerance in a genome-wide association study

Cited by 19 publications

References 61 publications

Genome wide association mapping for heat tolerance in sub-tropical maize

Genome wide association mapping for heat tolerance in sub-tropical maize

QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study

Achievements and prospects of molecular breeding for drought tolerance in soybean [Glycine max (L.) merr.]

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