Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars

Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a high-yielding but drought-susceptible cultivar, ‘Albany.’ The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. In silico expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.

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Detection of QTL underlying seed quality components in soybean [Glycine max (L.) Merr.]

Canadian Journal of Plant Science ◽

10.1139/cjps-2017-0204 ◽

2018 ◽

Vol 98 (4) ◽

pp. 881-888 ◽

Cited By ~ 4

Author(s):

Masum Akond ◽

Jiazheng Yuan ◽

Shiming Liu ◽

Stella K. Kantartzi ◽

Khalid Meksem ◽

...

Keyword(s):

Amino Acid ◽

Phenotypic Variation ◽

Seed Quality ◽

Snp Markers ◽

Seed Composition ◽

Single Nucleotide ◽

Glycine Max L ◽

Amino Acid Contents ◽

N 93 ◽

Major Qtl

Improving seed composition and quality, including protein, oil, fatty acid, and amino acid contents, is an important goal of soybean farmers and breeders. The aim of this study was to map the quantitative trait loci (QTL) underlying the contents of protein, oil, fatty acids, and amino acids with 1510 single nucleotide polymorphism (SNP) markers using the ‘Hamilton’ × ‘Spencer’ recombinant inbred line population (H × S; n = 93). A total of 13 QTL for the traits studied have been mapped on 3 chromosomes (Chr.) of the soybean genome. Three major QTL have been mapped to a 7–13 cM region on Chr. 6. One major QTL for oil content (qOIL001) explained approximately 76% of the total phenotypic variation in this population; the second major QTL for amino acid alanine (Ala; qALA001) explained approximately 74% of the total variation in Ala content; moreover, two major QTL for palmitic acid (qPAL001 and qPAL002) were identified on Chr. 6 and explained approximately 21% of the phenotypic variation in this population. The SNP markers flanking the QTL identified here will be very useful for soybean breeders to develop and select soybean lines with higher seed composition qualities using marker-assisted selection.

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Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers

Genes ◽

10.3390/genes12111690 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1690

Author(s):

Yheni Dwiningsih ◽

Anuj Kumar ◽

Julie Thomas ◽

Charles Ruiz ◽

Jawaher Alkahtani ◽

...

Keyword(s):

Candidate Genes ◽

High Throughput ◽

Inbred Line ◽

Recombinant Inbred Line ◽

Recombinant Inbred ◽

Genetic Information ◽

Snp Markers ◽

Rice Grain ◽

Grain Length ◽

Ril Population

Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of “Kaybonnet (KBNT lpa)” and “ZHE733” named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.

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Construction of a high density genetic map and QTL mapping of PEG-induced drought tolerance at the early seedling stage in sesame using whole genome re-sequencing

10.21203/rs.3.rs-50720/v2 ◽

2020 ◽

Author(s):

Junchao Liang ◽

Yanying Ye ◽

Xiaowen Yan ◽

Tingxian Yan ◽

Yueliang Rao ◽

...

Keyword(s):

Drought Tolerance ◽

Qtl Mapping ◽

Genetic Map ◽

Phenotypic Variation ◽

Root Length ◽

High Density ◽

Seedling Stage ◽

Whole Genome ◽

Major Qtls ◽

Ril Population

Abstract BackgroundImprovement in sesame (Sesamum indicum L.) drought tolerance at seedling stage is important for yield stability. Genetic approaches combing with conventional breeding is the most effective way to develop drought-tolerant cultivars. So far, only a few studies have been reported to reveal gene/ quantitative trait loci (QTL) controlling drought tolerance in sesame. To identify the genomic regions associated with drought tolerance, we constructed a high-density genetic map using a recombinant inbred line (RIL) population through whole genome re-sequencing (WGRS) technique. QTLs contributing to three seedling traits were identified under both non-stress and water stress conditions.ResultsThree drought tolerance related traits and their relative values (the ratio of value under stress to value under control condition), including seedling weight (SW), shoot length (SL) and root length (RL), were evaluated under control and PEG-induced osmotic conditions at seedling stage in a RIL population derived from cross of Zhushanbai (ZSB) and Jinhuangma (JHM). Significant variation and high broad sense heritability were observed for all traits except SW under stress condition in the population. With this population, a high-density linkage map with 1354 bin markers was constructed through WGRS strategy. Composite interval mapping analysis was performed for all the traits as well as their relative phenotypic data. A total of 34 QTLs were detected for these traits under both conditions and their relative values, and 13 stable QTLs associated with seven traits were revealed in two independent experiments, explaining on average, 4.95-16.26% of phenotypic variation for each QTL. Four of them contributed more than 10% of phenotypic variation. One region on chromosome 12 contained two major QTLs related to RL under osmotic condition and relative RL. Seven candidate genes underlying major QTLs for drought tolerance were identified according to gene descriptions and variations between parents.ConclusionThe current study reports the first QTL mapping of drought tolerance related traits through a RIL population and first QTL detection of root related trait (root length) in sesame. These findings will provide new genetic resources for molecular improvement of drought tolerance and candidate gene identification in sesame.

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Mapping and validation of a major QTL for primary root length of soybean seedlings grown in hydroponic conditions

BMC Genomics ◽

10.1186/s12864-021-07445-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Huatao Chen ◽

Giriraj Kumawat ◽

Yongliang Yan ◽

Baojie Fan ◽

Donghe Xu

Keyword(s):

Qtl Analysis ◽

Phenotypic Variation ◽

Root Length ◽

Primary Root ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Ril Population ◽

Hydroponic Conditions ◽

Primary Root Length ◽

Major Qtl

Abstract Background The root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative trait loci (QTL) associated with primary root length (PRL) during soybean seedling growth in hydroponic conditions. A total of 103 F7 recombinant inbred lines (RILs) derived from a cross between K099 (short primary root) and Fendou 16 (long primary root) were used to identify QTL for PRL in soybean. The RIL population was genotyped with 223 simple sequence repeats markers covering 20 chromosomes. Phenotyping for primary root length was performed for 3-weeks plants grown in hydoponic conditions. The identified QTL was validated in near isogenic lines and in a separate RIL population. Results QTL analysis using inclusive composite interval mapping method identified a major QTL on Gm16 between SSR markers Sat_165 and Satt621, explaining 30.25 % of the total phenotypic variation. The identified QTL, qRL16.1, was further confirmed in a segregating population derived from a residual heterozygous line (RHLs-98). To validate qRL16.1 in a different genetic background, QTL analysis was performed in another F6 RIL population derived from a cross between Union (medium primary root) and Fendou 16, in which a major QTL was detected again in the same genomic region as qRL16.1, explaining 14 % of the total phenotypic variation for PRL. In addition, the effect of qRL16.1 was confirmed using two pair of near-isogenic lines (NILs). PRL was significantly higher in NILs possessing the qRL16.1 allele from Fendou 16 compared to allele from K099. Conclusions The qRL16.1 is a novel QTL for primary root length in soybean which provides important information on the genetic control of root development. Identification of this major QTL will facilitate positional cloning and DNA marker-assisted selection for root traits in soybean.

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Construction of a High Density Genetic Map and QTL Mapping of PEG-Induced Drought Tolerance at Seedling Stage in Sesame Using Whole Genome Re-Sequencing

10.21203/rs.3.rs-50720/v1 ◽

2020 ◽

Author(s):

Junchao Liang ◽

Yanying Ye ◽

Xiaowen Yan ◽

Tingxian Yan ◽

Yueliang Rao ◽

...

Keyword(s):

Drought Tolerance ◽

Qtl Mapping ◽

Genetic Map ◽

Phenotypic Variation ◽

Root Length ◽

High Density ◽

Seedling Stage ◽

Whole Genome ◽

Phenotypic Data ◽

Ril Population

Abstract BackgroundImprovement in sesame (Sesamum indicum L.) drought tolerance at seedling stage is important for yield stability. Genetic approaches combing with conventional breeding is the most effective way to develop drought-tolerant cultivars. So far, very few studies have been reported to reveal gene/ quantitative trait loci (QTL) controlling drought tolerance in sesame. To identify the genomic regions associated with drought tolerance, we constructed a high-density genetic map using a recombinant inbred line (RIL) population through whole genome re-sequencing (WGRS) technique. QTLs contributing to three seedling traits were identified under both non-stress and water stress conditions.ResultsThree drought tolerance related traits and their relative values (the ratio of value under stress to value under control condition), including seedling weight (SW), shoot length (SL) and root length (RL), were evaluated under control and PEG-induced osmotic conditions at seedling stage in a RIL population derived from cross of Zhushanbai (ZSB) and Jinhuangma (JHM). Significant variation and high broad sense heritability were observed for all traits except SW under stress condition in the population. With this population, a high-density linkage map with 1354 bin markers was constructed through WGRS strategy. Composite interval mapping analysis was performed for all the traits as well as their relative phenotypic data. A total of 34 QTLs were detected for these three traits under both conditions and their relative values, and 13 stable QTLs associated with seven traits could be revealed in two independent experiments, explaining on average, 4.95-16.26% of phenotypic variation for each QTL. Four of them contributed more than 10% of phenotypic variation. Root length related QTLs were first identified in sesame. One region on chromosome 12 contained two major QTLs related to RL under osmotic condition and relative RL. ConclusionThe current study reports the first QTL mapping of drought tolerance related traits through a RIL population and first QTL detection of root related trait (root length) in sesame. These findings will provide new genetic resources for molecular improvement of drought tolerance and candidate gene identification in sesame.

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Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance

Genome Biology ◽

10.1186/s13059-021-02377-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xi Wu ◽

Hui Feng ◽

Di Wu ◽

Shijuan Yan ◽

Pei Zhang ◽

...

Keyword(s):

Drought Tolerance ◽

Candidate Genes ◽

High Throughput ◽

Complex Traits ◽

Genetic Architecture ◽

World Population ◽

Eqtl Analysis ◽

New Genes ◽

Computed Tomography Images ◽

Drought Tolerant

Abstract Background Drought threatens the food supply of the world population. Dissecting the dynamic responses of plants to drought will be beneficial for breeding drought-tolerant crops, as the genetic controls of these responses remain largely unknown. Results Here we develop a high-throughput multiple optical phenotyping system to noninvasively phenotype 368 maize genotypes with or without drought stress over a course of 98 days, and collected multiple optical images, including color camera scanning, hyperspectral imaging, and X-ray computed tomography images. We develop high-throughput analysis pipelines to extract image-based traits (i-traits). Of these i-traits, 10,080 were effective and heritable indicators of maize external and internal drought responses. An i-trait-based genome-wide association study reveals 4322 significant locus-trait associations, representing 1529 quantitative trait loci (QTLs) and 2318 candidate genes, many that co-localize with previously reported maize drought responsive QTLs. Expression QTL (eQTL) analysis uncovers many local and distant regulatory variants that control the expression of the candidate genes. We use genetic mutation analysis to validate two new genes, ZmcPGM2 and ZmFAB1A, which regulate i-traits and drought tolerance. Moreover, the value of the candidate genes as drought-tolerant genetic markers is revealed by genome selection analysis, and 15 i-traits are identified as potential markers for maize drought tolerance breeding. Conclusion Our study demonstrates that combining high-throughput multiple optical phenotyping and GWAS is a novel and effective approach to dissect the genetic architecture of complex traits and clone drought-tolerance associated genes.

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Photochemical efficiency correlated with candidate gene expression promote coffee drought tolerance

Scientific Reports ◽

10.1038/s41598-021-86689-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Meline de Oliveira Santos ◽

Larissa Sousa Coelho ◽

Gladyston Rodrigues Carvalho ◽

Cesar Elias Botelho ◽

Luana Ferreira Torres ◽

...

Keyword(s):

Drought Tolerance ◽

Candidate Genes ◽

Water Deficit ◽

Water Status ◽

Photochemical Efficiency ◽

Regulatory Proteins ◽

Drought Tolerant ◽

Major Response ◽

Genes Expression ◽

Response To Stress

AbstractThe aim of this study was to identify the correlation between photochemical efficiency and candidate genes expression to elucidate the drought tolerance mechanisms in coffee progenies (Icatu Vermelho IAC 3851-2 × Catimor UFV 1602-215) previously identified as tolerant in field conditions. Four progenies (2, 5, 12 and 15) were evaluated under water-deficit conditions (water deficit imposed 8 months after transplanting seedlings to the pots) and under irrigated system. Evaluations of physiological parameters and expression of candidate genes for drought tolerance were performed. Progeny 5 showed capacity to maintain water potential, which contributed to lower qP variation between irrigated and deficit conditions. However, the increases of qN and NPQ in response to stress indicate that this progeny is photochemically responsive to small variations of Ψam protecting the photosystem and maintaining qP. Data obtained for progeny 12 indicated a lower water status maintenance capacity, but with increased qN and NPQ providing maintenance of the ɸPSII and ETR parameters. A PCA analysis revealed that the genes coding regulatory proteins, ABA-synthesis, cellular protectors, isoforms of ascorbate peroxidase clearly displayed a major response to drought stress and discriminated the progenies 5 and 12 which showed a better photochemical response. The genes CaMYB1, CaERF017, CaEDR2, CaNCED, CaAPX1, CaAPX5, CaGolS3, CaDHN1 and CaPYL8a were up-regulated in the arabica coffee progenies with greater photochemical efficiency under deficit and therefore contributing to efficiency of the photosynthesis in drought tolerant progenies.

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Does susceptibility to heat stress confound screening for drought tolerance in rice?

Functional Plant Biology ◽

10.1071/fp10224 ◽

2011 ◽

Vol 38 (4) ◽

pp. 261 ◽

Cited By ~ 28

Author(s):

Krishna S. V. Jagadish ◽

Jill E. Cairns ◽

Arvind Kumar ◽

Impa M. Somayanda ◽

Peter Q. Craufurd

Keyword(s):

Heat Stress ◽

Drought Tolerance ◽

Candidate Genes ◽

Tissue Temperature ◽

Drought Tolerant ◽

Hot Season ◽

Dry Seasons ◽

Drought And Heat Stress ◽

Drought Screening ◽

Mapping Populations

Drought affected rice areas are predicted to double by the end of this century, demanding greater tolerance in widely adapted mega-varieties. Progress on incorporating better drought tolerance has been slow due to lack of appropriate phenotyping protocols. Furthermore, existing protocols do not consider the effect of drought and heat interactions, especially during the critical flowering stage, which could lead to false conclusion about drought tolerance. Screening germplasm and mapping-populations to identify quantitative trait loci (QTL)/candidate genes for drought tolerance is usually conducted in hot dry seasons where water supply can be controlled. Hence, results from dry season drought screening in the field could be confounded by heat stress, either directly on heat sensitive processes such as pollination or indirectly by raising tissue temperature through reducing transpirational cooling under water deficit conditions. Drought-tolerant entries or drought-responsive candidate genes/QTL identified from germplasm highly susceptible to heat stress during anthesis/flowering have to be interpreted with caution. During drought screening, germplasm tolerant to water stress but highly susceptible to heat stress has to be excluded during dry and hot season screening. Responses to drought and heat stress in rice are compared and results from field and controlled environment experiments studying drought and heat tolerance and their interaction are discussed.

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Genome-Wide Association Mapping for Yield and Related Traits Under Drought Stressed and Non-stressed Environments in Wheat

Frontiers in Genetics ◽

10.3389/fgene.2021.649988 ◽

2021 ◽

Vol 12 ◽

Author(s):

S. M. Hisam A. Rabbi ◽

Ajay Kumar ◽

Sepehr Mohajeri Naraghi ◽

Senay Simsek ◽

Suraj Sapkota ◽

...

Keyword(s):

Drought Tolerance ◽

Association Mapping ◽

Spring Wheat ◽

Mixed Linear Model ◽

Kernel Weight ◽

The Novel ◽

Hard Red Spring Wheat ◽

Drought Tolerant ◽

Genome Wide ◽

Days To Heading

Understanding the genetics of drought tolerance in hard red spring wheat (HRSW) in northern USA is a prerequisite for developing drought-tolerant cultivars for this region. An association mapping (AM) study for drought tolerance in spring wheat in northern USA was undertaken using 361 wheat genotypes and Infinium 90K single-nucleotide polymorphism (SNP) assay. The genotypes were evaluated in nine different locations of North Dakota (ND) for plant height (PH), days to heading (DH), yield (YLD), test weight (TW), and thousand kernel weight (TKW) under rain-fed conditions. Rainfall data and soil type of the locations were used to assess drought conditions. A mixed linear model (MLM), which accounts for population structure and kinship (PC+K), was used for marker–trait association. A total of 69 consistent QTL involved with drought tolerance-related traits were identified, with p ≤ 0.001. Chromosomes 1A, 3A, 3B, 4B, 4D, 5B, 6A, and 6B were identified to harbor major QTL for drought tolerance. Six potential novel QTL were identified on chromosomes 3D, 4A, 5B, 7A, and 7B. The novel QTL were identified for DH, PH, and TKW. The findings of this study can be used in marker-assisted selection (MAS) for drought-tolerance breeding in spring wheat.

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