Rapid identification and characterization of genetic loci for defective kernel in bread wheat

Abstract Background Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78 - 18.17%, 16.61 - 21.83% and 19.08 - 28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were determined according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions Overall, we achieved a rapid QTL mapping and reasonable predication of causal genes for Dek, laying foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.

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Rapid identification and characterization of genetic loci for defective kernel in bread wheat

10.21203/rs.2.11611/v2 ◽

2019 ◽

Author(s):

Chao Fu ◽

Jiuyuan Du ◽

Xiuling Tian ◽

Zhonghu He ◽

Luping Fu ◽

...

Keyword(s):

Wheat Yield ◽

Grain Filling ◽

Rapid Identification ◽

Snp Markers ◽

Yield Potential ◽

Genetic Population ◽

Polymorphic Snps ◽

Causal Genes ◽

Biochemical Analyses ◽

World Food Security

Abstract Background Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78 - 18.17%, 16.61 - 21.83% and 19.08 - 28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were determined according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions Overall, we achieved a rapid QTL mapping and reasonable predication of causal genes for Dek, laying foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.

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Rapid identification and characterization of genetic loci for defective kernel in bread wheat

BMC Plant Biology ◽

10.1186/s12870-019-2102-6 ◽

2019 ◽

Vol 19 (1) ◽

Author(s):

Chao Fu ◽

Jiuyuan Du ◽

Xiuling Tian ◽

Zhonghu He ◽

Luping Fu ◽

...

Keyword(s):

Wheat Yield ◽

Grain Filling ◽

Rapid Identification ◽

Snp Markers ◽

Yield Potential ◽

Genetic Population ◽

Polymorphic Snps ◽

Causal Genes ◽

Biochemical Analyses ◽

World Food Security

Abstract Background Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78–18.17%, 16.61–21.83% and 19.08–28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were predicated according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions Three major QTL for Dek were identified and their causal genes were predicted, laying a foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.

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Rapid identification and characterization of genetic loci for defective kernel in bread wheat

10.21203/rs.2.11611/v5 ◽

2019 ◽

Author(s):

Chao Fu ◽

Jiuyuan Du ◽

Xiuling Tian ◽

Zhonghu He ◽

Luping Fu ◽

...

Keyword(s):

Wheat Yield ◽

Grain Filling ◽

Rapid Identification ◽

Snp Markers ◽

Yield Potential ◽

Genetic Population ◽

Polymorphic Snps ◽

Causal Genes ◽

Biochemical Analyses ◽

World Food Security

Abstract Background Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78 - 18.17%, 16.61 - 21.83% and 19.08 - 28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were determined according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions Overall, we achieved a rapid QTL mapping and reasonable predication of causal genes for Dek, laying foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.

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Rapid identification and characterization of genetic loci for defective kernel in bread wheat

10.21203/rs.2.11611/v4 ◽

2019 ◽

Author(s):

Chao Fu ◽

Jiuyuan Du ◽

Xiuling Tian ◽

Zhonghu He ◽

Luping Fu ◽

...

Keyword(s):

Wheat Yield ◽

Grain Filling ◽

Rapid Identification ◽

Snp Markers ◽

Yield Potential ◽

Genetic Population ◽

Polymorphic Snps ◽

Causal Genes ◽

Biochemical Analyses ◽

World Food Security

Abstract Background Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78 - 18.17%, 16.61 - 21.83% and 19.08 - 28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were determined according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions Overall, we achieved a rapid QTL mapping and reasonable predication of causal genes for Dek, laying foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.

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An assessment of wheat yield sensitivity and breeding gains in hot environments

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.2190 ◽

2013 ◽

Vol 280 (1752) ◽

pp. 20122190 ◽

Cited By ~ 62

Author(s):

Sharon M. Gourdji ◽

Ky L. Mathews ◽

Matthew Reynolds ◽

José Crossa ◽

David B. Lobell

Keyword(s):

Heat Tolerance ◽

Wheat Yield ◽

Vapour Pressure Deficit ◽

Grain Filling ◽

Yield Potential ◽

High Yield ◽

Genetic Gains ◽

Yield Trial ◽

Hot Environments ◽

Over Time

Genetic improvements in heat tolerance of wheat provide a potential adaptation response to long-term warming trends, and may also boost yields in wheat-growing areas already subject to heat stress. Yet there have been few assessments of recent progress in breeding wheat for hot environments. Here, data from 25 years of wheat trials in 76 countries from the International Maize and Wheat Improvement Center (CIMMYT) are used to empirically model the response of wheat to environmental variation and assess the genetic gains over time in different environments and for different breeding strategies. Wheat yields exhibited the most sensitivity to warming during the grain-filling stage, typically the hottest part of the season. Sites with high vapour pressure deficit (VPD) exhibited a less negative response to temperatures during this period, probably associated with increased transpirational cooling. Genetic improvements were assessed by using the empirical model to correct observed yield growth for changes in environmental conditions and management over time. These ‘climate-corrected’ yield trends showed that most of the genetic gains in the high-yield-potential Elite Spring Wheat Yield Trial (ESWYT) were made at cooler temperatures, close to the physiological optimum, with no evidence for genetic gains at the hottest temperatures. In contrast, the Semi-Arid Wheat Yield Trial (SAWYT), a lower-yielding nursery targeted at maintaining yields under stressed conditions, showed the strongest genetic gains at the hottest temperatures. These results imply that targeted breeding efforts help us to ensure progress in building heat tolerance, and that intensified (and possibly new) approaches are needed to improve the yield potential of wheat in hot environments in order to maintain global food security in a warmer climate.

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Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽

10.3390/genes12071042 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1042

Author(s):

Zhuoying Weng ◽

Yang Yang ◽

Xi Wang ◽

Lina Wu ◽

Sijie Hua ◽

...

Keyword(s):

Fishery Management ◽

Genotyping By Sequencing ◽

Parentage Analysis ◽

Snp Markers ◽

Individual Identification ◽

Pedigree Information ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Polymorphic Snps ◽

Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

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SUMMARY: PAPERS PRESENTED AT INTERNATIONAL WORKSHOP ON INCREASING WHEAT YIELD POTENTIAL, CIMMYT, OBREGON, MEXICO, 20–24 MARCH 2006 Challenges to international wheat improvement

The Journal of Agricultural Science ◽

10.1017/s0021859607007034 ◽

2007 ◽

Vol 145 (3) ◽

pp. 223-227 ◽

Cited By ~ 16

Author(s):

M. P. REYNOLDS ◽

P. R. HOBBS ◽

H. J. BRAUN

Keyword(s):

Management Practices ◽

International Workshop ◽

Green Revolution ◽

Wheat Yield ◽

Developed Countries ◽

Yield Potential ◽

Agronomic Practices ◽

Agronomic Management ◽

Genetically Improved ◽

New Generation

Wheat is grown on 210 million ha throughout the world producing approximately 600 million tonnes of grain (10 year average; FAO 2005) and providing on average one fifth of the total calorific input of the world's population (FAO 2003). For some regions such as North Africa, Turkey and Central Asia, wheat provides half of total dietary energy intake. Of the cultivated wheat area, half is located in less developed countries where there have been steady increases in productivity since the green revolution, associated with genetic improvements in yield potential, resistance to diseases and adaptation to abiotic stresses (Reynolds & Borlaug 2006a, b) as well as better agronomic practices (Derpsch 2005). Nonetheless, challenges to wheat production are still considerable, especially in the developing world, not only because of increased demand but also because of the increased scarcity of water resources (Rosegrant 1997; WMO 1997), ever more unpredictable climates (Fischer et al. 2002), increased urbanization and loss of good quality land away from agriculture (Hobbs 2007), and decreased public sector investment in agriculture and rural affairs (Falcon & Naylor 2005). To meet demand in a sustainable way, more resources are required to breed a new generation of genetically improved cultivars as well as implement resource-conserving agronomic management practices.

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Over-Optimistic Projected Future Wheat Yield Potential in the North China Plain: The Role of Future Climate Extremes

Agronomy ◽

10.3390/agronomy12010145 ◽

2022 ◽

Vol 12 (1) ◽

pp. 145

Author(s):

Rui Yang ◽

Panhong Dai ◽

Bin Wang ◽

Tao Jin ◽

Ke Liu ◽

...

Keyword(s):

Drought Stress ◽

North China Plain ◽

North China ◽

Crop Yields ◽

Wheat Yield ◽

Yield Potential ◽

Severe Drought ◽

The North ◽

The North China Plain ◽

Stress Environments

Global warming and altered precipitation patterns pose a serious threat to crop production in the North China Plain (NCP). Quantifying the frequency of adverse climate events (e.g., frost, heat and drought) under future climates and assessing how those climatic extreme events would affect yield are important to effectively inform and make science-based adaptation options for agriculture in a changing climate. In this study, we evaluated the effects of heat and frost stress during sensitive phenological stages at four representative sites in the NCP using the APSIM-wheat model. climate data included historical and future climates, the latter being informed by projections from 22 Global Climate Models (GCMs) in the Coupled Model Inter-comparison Project phase 6 (CMIP6) for the period 2031–2060 (2050s). Our results show that current projections of future wheat yield potential in the North China Plain may be overestimated; after more accurately accounting for the effects of frost and heat stress in the model, yield projections for 2031-60 decreased from 31% to 9%. Clustering of common drought-stress seasonal patterns into key groups revealed that moderate drought stress environments are likely to be alleviated in the future, although the frequency of severe drought-stress environments would remain similar (25%) to that occurring under the current climate. We highlight the importance of mechanistically accounting for temperature stress on crop physiology, enabling more robust projections of crop yields under future the burgeoning climate crisis.

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Influence of meteorological parameters on wheat yield under different sowing conditions

MAUSAM ◽

10.54302/mausam.v73i1.5089 ◽

2022 ◽

Vol 73 (1) ◽

pp. 161-172

Author(s):

ANANTA VASHISTH ◽

DEBASISH ROY ◽

AVINASH GOYAL ◽

P. KRISHNAN

Keyword(s):

Relative Humidity ◽

Soil Temperature ◽

Air Temperature ◽

Field Experiments ◽

Wheat Yield ◽

Weather Condition ◽

Grain Filling ◽

Crop Growth ◽

Leaf Water ◽

Growth Stages

Field experiments were conducted on the research farm of IARI, New Delhi during Rabi 2016-17 and 2017-18. Three varieties of wheat (PBW-723, HD-2967 and HD-3086) were sown on three different dates for generating different weather condition during various phenological stages of crop. Results showed that during early crop growth stages soil moisture had higher value and soil temperature had lower value and with progress of crop growth stage, the moisture in the upper layer decreased and soil temperature increased significantly as compared to the bottom layers. During tillering and jointing stage, air temperature within canopy was more and relative humidity was less while during flowering and grain filling stage, air temperature within canopy was less and relative humidity was more in timely sown crop as compared to late and very late sown crop. Radiation use efficiency and relative leaf water content had significantly higher value while leaf water potential had lower value in timely sown crop followed by late and very late sown crop. Yield had higher value in HD-3086 followed by HD-2967 and PBW-723 in all weather conditions. Canopy air temperature difference had positive value in very late sown crop particularly during flowering and grain-filling stages. This reflects in the yield. Yield was more in timely sown crop as compared to late and very late sown crop.

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