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Molecular Markers and Marker-Assisted Breeding in Wheat

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A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Genotype Evaluation and Breeding".

Deadline for manuscript submissions: closed (15 December 2022) | Viewed by 14172

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Special Issue Editors

Prof. Dr. Aimin Zhang

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Guest Editor

State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding 071000, Hebei, China
Interests: wheat molecular breeding; wheat genomics; wheat male sterility and heterosis; yield potential improvement; generation accelerating technology; genomic selection

Prof. Dr. Dongcheng Liu

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Guest Editor

State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding 071000, Hebei, China
Interests: wheat quality improvement; wheat proteomics; QTL mapping; wheat genomics

Prof. Dr. Xianchun Xia

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Guest Editor

1. Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
2. Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China
Interests: wheat molecular markers development; functional markers; disease resistance; wheat genomics

Special Issue Information

Dear Colleagues,

Wheat, as a dominant cereal crop, is one of the most important staple foods. In 2020/2021, it was grown on about 219 million hectares of land, with around 764 million metric tons of grain being produced worldwide. Globally, 19% of the calorie demand and 20% of the protein demand are fulfilled by wheat production. Thanks to the development of new varieties by advanced breeding technology, especially using molecular markers in breeding, which greatly facilitate the selection process, the yield potential of wheat has increased significantly. The global population is expected to reach 9.8 billion by 2050, and an annual gain of ~2% in grain yield and a ~50% cumulative increase in the next 20 years are necessary to meet the predicted demand. Increasing the yield per unit area, improving the quality, and making crops more resilient to climate change by genetic improvement is the only way to meet this demand. Molecular markers and molecular assisted breeding will become more and more important in wheat genetic improvement to ensure human food security.

Prof. Dr. Aimin Zhang
Prof. Dr. Dongcheng Liu
Prof. Dr. Xianchun Xia
Guest Editors

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Keywords

wheat
molecular markers
marker assisted breeding
yield improvement
disease resistance
quality improvement
resilience to climate change
human food security

Published Papers (6 papers)

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Research

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10 pages, 2188 KiB

Open AccessArticle

Broad-Spectrum Resistance to Leaf Rust in the Argentinean Wheat Cultivar “Klein Proteo” Is Controlled by LrKP Located on Chromosome 2BS

by Shengsheng Bai, Shuyong Pang, Hongna Li, Jinwei Yang, Haitao Yu, Shisheng Chen and Xiaodong Wang

Agriculture 2022, 12(11), 1836; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture12111836 - 02 Nov 2022

Cited by 1 | Viewed by 1228

Abstract

Wheat leaf rust, caused by Puccinia triticina, is a severe fungal disease threatening global wheat production. The rational application of genetic loci controlling wheat resistance to leaf rust in breeding practice is still the best choice for disease control. A previous study indicated that the Argentinean wheat cultivar “Klein Proteo” might carry leaf rust resistance (Lr) genes Lr3a and Lr10, as well as an unknown Lr gene. In this study, seedlings of “Klein Proteo” showed high resistance to all the 20 Pt pathotypes isolated in China. Using bulked segregant RNA sequencing (BSR-seq) and developed CAPS markers, the single-dominant gene LrKP was initially mapped to a 114–168 Mb region on chromosome 2BS. Using gene-specific primers of a previously cloned chromosome 2BS-located Lr13 gene, we found that “Klein Proteo” also carried the Lr13 gene. Moreover, the expression of Lr13 in the resistant bulk was significantly higher than that in the susceptible bulk. Nevertheless, “Klein Proteo” showed a much broader and higher resistance compared with the near isogenic line and “ZhouMai 22” carrying Lr13. In conclusion, the wheat cultivar “Klein Proteo” showed great potential in the genetic improvement of wheat resistance to leaf rust in China and the genetic bases controlling the broad-spectrum resistance were initially revealed. Full article

(This article belongs to the Special Issue Molecular Markers and Marker-Assisted Breeding in Wheat)

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18 pages, 1126 KiB

Open AccessArticle

Traditional and Conditional QTL Analysis of Kernel Size- and Shape-Related Traits in Wheat (Triticum aestivum L.)

by Xiaoli Fan, Xiaofeng Liu, Shaodan Guo, Bo Feng, Qiang Zhou, Guangbing Deng, Hai Long, Zhibin Xu and Tao Wang

Agriculture 2022, 12(10), 1718; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture12101718 - 18 Oct 2022

Viewed by 1327

Abstract

Optimal kernel size and shape were critical in improving the wheat yield potential and processing quality. A traditional and conditional QTL analysis for kernel-related traits was performed using 152 recombinant inbred lines derived from a cross between Zhongkemai 138 (ZKM138) and Kechengmai 2, whose kernel size showed significant differences. A total of 48 traditional QTLs (LOD: 3.69–14.20) were identified, with twenty-six QTLs distributed across five genomic regions. Each had at least one major stable QTL for kernel-related traits. We deduced from the co-location and conditional QTL analysis results that R3D and R4B.1 primarily controlled kernel shape, while R4D, R6A, and R6D2 primarily contributed to kernel size and the final thousand-kernel weight, potentially providing the genetic basis for the ZKM138’s high TKW and large-kernel performance. R4D may be involved with Rht2, and the possible regulatory effects of the other four QTL clusters are more likely to be influenced by unknown genes. The KASP markers validated their effect on kernel-related traits, and they were used to analyze the transmissibility and distribution of superior genotypes in ZKM138 derivatives and global wheat cultivars, respectively. These findings may serve as a reference for future genetic improvement of the ideal kernel morphology. Full article

(This article belongs to the Special Issue Molecular Markers and Marker-Assisted Breeding in Wheat)

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15 pages, 3401 KiB

Open AccessArticle

Identification and Validation of Quantitative Trait Loci for Grain Size in Bread Wheat (Triticum aestivum L.)

by Wenjing Hu, Sen Liao, Die Zhao, Jizeng Jia, Weigang Xu and Shunhe Cheng

Agriculture 2022, 12(6), 822; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture12060822 - 08 Jun 2022

Cited by 6 | Viewed by 2003

Abstract

Grain width (GW) and grain length (GL) are crucial components affecting grain weight. Dissection of their genetic control is essential for improving yield potential in wheat breeding. Yangmai 12 (YM12) and Yanzhan 1 (YZ1) are two elite cultivars released in the Middle and Lower Yangtze Valleys Wheat Zone (MLYVWZ) and the Yellow-Huai River Valleys Wheat Zone (YRVWZ), respectively. One biparental population derived from YM12/YZ1 cross was employed to perform QTL mapping based on the data from four environments over two years to detect quantitative trait loci (QTL) for GW and GL. A total of eight QTL were identified on chromosomes 1B, 2D, 3B, 4B, 5A, and 6B. Notably, QGW.yz.2D was co-located with QGL.yz.2D, and QGW.yz.4B was co-located with QGL.yz.4B, respectively. QGW.yz.2D and QGL.yz.2D, with the increasing GW/GL allele from YZ1, explained 12.36–18.27% and 13.69–26.53% of the phenotypic variations for GW and GL, respectively. QGW.yz.4B and QGL.yz.4B, with the increasing GW/GL allele from YM12, explained 10.34–11.95% and 10.35–16.04% of the phenotypic variation for GW and GL, respectively. QGL.yz.5A, with the increasing GL allele from YM12, explained 10.04–12.48% of the phenotypic variation for GL. Moreover, the positive alleles of these three QTL regions could significantly increase thousand-grain weight, and QGW.yz.4B/QGL.yz.4B and QGL.yz.5A did not show significant negative effects on grain number per spike. QGL.yz.2D, QGW.yz.4B/QGL.yz.4B, and QGL.yz.5A have not been reported. These three QTL regions were then further validated using Kompetitive Allele-Specific PCR (KASP) markers in 159 wheat cultivars/lines from MLYVWZ and YRVWZ. Combining the positive alleles of the major QTL significantly increased GW and GL. Eleven candidate genes associated with encoding ethylene-responsive transcription factor, oleosin, osmotin protein, and thaumatin protein were identified. Three major QTL and KASP markers reported here will be helpful in developing new wheat cultivars with high and stable yields. Full article

(This article belongs to the Special Issue Molecular Markers and Marker-Assisted Breeding in Wheat)

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16 pages, 2800 KiB

Open AccessArticle

An Analysis of the Genetic Relation between Photosynthesis and Yield-Related Traits in Wheat

by Qiang An, Chunlian Li, Hongwei Li, Qi Zheng, Bin Li and Zhensheng Li

Agriculture 2022, 12(4), 560; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture12040560 - 14 Apr 2022

Cited by 5 | Viewed by 2056

Abstract

A recombinant inbred line population, derived from a cross between a high light-tolerant wheat Triticum aestivum cv. Xiaoyan 54 and a high yielding, but high light-sensitive variety, Jing 411, was used to explore the genetic relation between photosynthesis and grain yield-related traits. The net CO₂ assimilation rate, chlorophyll content, chlorophyll a fluorescence parameters, leaf area index, plant height, spike number, biomass, grain yield, and harvest index were evaluated in the field across two consecutive years. The results reveal that a total of 57 quantitative trait loci (QTL) are found to be associated with the investigated traits. They distributed on almost all 21 chromosomes, except for chromosomes 5D, 6D, 7A, and 7D. The phenotypic variance explained by a single QTL ranged from 9.3% to 39.9% depending on traits and QTL. Of these QTL, 12 QTL clusters were found to regulate at least 2 of the investigated traits, which distributed on 8 chromosomes, 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4B and 5A. Seven QTL clusters were associated with both photosynthesis and grain yield-related traits, indicative of their genetic relation. Two QTL clusters on 2D and 4B were co-located with two reduced-height genes, Rht8 and Rht-B1b, respectively. These QTL clusters may be used as potential targets for wheat radiation use efficiency improvement in the future. Full article

(This article belongs to the Special Issue Molecular Markers and Marker-Assisted Breeding in Wheat)

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9 pages, 978 KiB

Open AccessArticle

Establishment and Application of Multiplex PCR Systems Based on Molecular Markers for HMW-GSs in Wheat

by Chuxuan Yao, Cuimian Zhang, Caili Bi, Shuo Zhou, Fushuang Dong, Yongwei Liu, Fan Yang, Bo Jiao, He Zhao, Mengyu Lyu, Haibo Wang and Jianfang Chai

Agriculture 2022, 12(4), 556; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture12040556 - 13 Apr 2022

Cited by 4 | Viewed by 1824

Abstract

High-molecular-weight glutenin subunits (HMW-GSs) encoded by alleles at the Glu-A1, Glu-B1, and Glu-D1 loci confer unique end-use quality properties of common wheat (Triticum aestivum L.). Wheat accessions with the high-quality HMW-GSs combination of Ax2*/Bx7^OE/Dx5 usually exhibit strong gluten characteristics. In order to stack these three high-quality subunit genes by molecular markers in strong gluten wheat breeding, an agarose gel-based multiplex PCR marker for these high-quality HMW-GSs and two agarose gel-based multiplex PCR markers detecting the homozygosity of Ax2* and Bx7^OE subunits were developed. These markers were verified in an F₂ segregating population from a cross between a medium-gluten winter wheat cultivar with the HMW-GSs combination of Ax null/Bx7 + By8/Dx4 + Dy12 and a strong-gluten spring wheat cultivar with the HMW-GSs combination of Ax2*/Bx7^OE + By8*/Dx5 + Dy10. By integrating the newly established multiplex PCR markers and a published co-dominant PCR marker of the Dx5 subunit, a complete molecular marker selection system was established. After multiple rounds of molecular marker-assisted selection with the system, 17 homozygous winter wheat lines that stacked the three high-quality HMW-GSs were generated. The gluten strength of these homozygous lines was comparable to their strong-gluten parent, but significantly higher than that of their medium-gluten parent by measuring their lactic acid-sodium dodecyl sulfate solvent retention capacities of whole wheat meal. The multiplex PCR systems established in the present study can be used for molecular marker-assisted selection of strong gluten wheats. Full article

(This article belongs to the Special Issue Molecular Markers and Marker-Assisted Breeding in Wheat)

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Review

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18 pages, 794 KiB

Open AccessReview

Molecular Markers and Their Applications in Marker-Assisted Selection (MAS) in Bread Wheat (Triticum aestivum L.)

by Liqiang Song, Ruihui Wang, Xueju Yang, Aimin Zhang and Dongcheng Liu

Agriculture 2023, 13(3), 642; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture13030642 - 08 Mar 2023

Cited by 9 | Viewed by 4228

Abstract

As one of the essential cereal crops, wheat provides 20% of the calories and proteins consumed by humans. Due to population expansion, dietary shift and climate change, it is challenging for wheat breeders to develop new varieties for meeting wheat production requirements. Marker-assisted selection (MAS) has distinct advantages over conventional selection in plant breeding, such as being time-saving, cost-effective and goal-oriented. This review makes attempts to give a description of different molecular markers: sequence tagged site (STS), simple sequence repeat (SSR), genotyping by sequencing (GBS), single nucleotide polymorphism (SNP) arrays, exome capture, Kompetitive Allele Specific PCR (KASP), cleaved amplified polymorphic sequence (CAPS), semi-thermal asymmetric reverse PCR (STARP) and genotyping by target sequencing (GBTS). We also summarize some quantitative trait loci (QTL)/genes as well as their linked markers, which are potentially useful in MAS. This paper provides updated information on some markers linked to critical traits and their potential applications in wheat breeding programs. Full article

(This article belongs to the Special Issue Molecular Markers and Marker-Assisted Breeding in Wheat)

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