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Identification and Validation of Quantitative Trait Loci for Important Agronomic...
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Identification and Validation of Quantitative Trait Loci for Important Agronomic Traits in Food Crops

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 August 2023) | Viewed by 12509

Special Issue Editors

Dr. Tianheng Ren

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Guest Editor
Provincial Key Laboratory for Plant Genetics and Breeding, Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
Interests: plant biology; wheat breeding; chromosome translocation; genome engineering
Prof. Dr. Pengtao Ma

E-Mail Website
Guest Editor
School of Life Sciences, Yantai University, Yantai 264005, China
Interests: wheat disease; molecular breeding; gene cloning
Special Issues, Collections and Topics in MDPI journals
Dr. Fahimeh Shahinnia

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Guest Editor
Research Scientist, Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, 85354 Freising, Germany
Interests: QTL mapping; genome-wide association mapping; disease resistance and abiotic stress tolerance; wheat; barley; plant genetics; molecular breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A quantitative trait is generally controlled by several genes, and the effect of each gene responsible for a quantitative trait is typically small. Therefore, quantitative traits are usually detected by quantitative trait loci (QTL) or genome-wide association (GWAS) analyses. Wheat, rice, and maize are the most important food crops in the world. The important agronomic traits of these food crops, such as plant height, thousand kernel weight, tiller number, kernel number per spike, and even several resistance traits, are typical quantitative traits. The analysis of these quantitative traits is of great significance for ensuring the high yield, disease resistance, as well as marker-assisted selection (MAS) of food crops. The objective of this Special Issue is to publish articles detailing progress in research involving QTL or GWAS analyses of food crops. Review and original research articles are both welcome on the following topics of interest:

  • QTL analysis of important agronomic or disease resistance traits of food crops (wheat, rice, and maize).
  • GWAS analysis of important agronomic or disease resistance traits of food crops (wheat, rice, and maize).
  • Meta-QTL analysis of important agronomic or disease resistance traits of food crops (wheat, rice, and maize).
  • New methods/new phenotyping tools/new genomic tools/new strategies aimed at increasing resolution in the detection of QTL in food crops.
  • Molecular marker design and validation of QTL.

Dr. Tianheng Ren
Dr. Pengtao Ma
Dr. Fahimeh Shahinnia
Guest Editors

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • QTL
  • GWAS
  • MAS
  • mapping
  • wheat
  • rice
  • maize
  • agronomic traits
  • disease resistance traits

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Published Papers (6 papers)

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Research

12 pages, 1827 KiB  
Article
QTL Mapping of Zeaxanthin Content in Sweet Corn Using Recombinant Inbred Line Population across Different Environments
by Yahui Zhang, Yunqi Tang, Weicai Jin, Yu Liu, Guangyu Li, Wenhao Zhong, Jun Huang and Wenyi Wang
Plants 2023, 12(19), 3506; https://doi.org/10.3390/plants12193506 - 9 Oct 2023
Cited by 1 | Viewed by 1234
Abstract
Zeaxanthin is a naturally occurring xanthophyll carotenoid obtained from diet sources. Particularly, sweet corn is a major source of dietary zeaxanthin. To investigate the genetic basis of zeaxanthin content regulation in sweet corn, a recombinant inbred line (RIL) population comprising 191 families was [...] Read more.
Zeaxanthin is a naturally occurring xanthophyll carotenoid obtained from diet sources. Particularly, sweet corn is a major source of dietary zeaxanthin. To investigate the genetic basis of zeaxanthin content regulation in sweet corn, a recombinant inbred line (RIL) population comprising 191 families was constructed using two inbred lines (K44 and F22) with contrasting zeaxanthin content in the grain. The zeaxanthin content in the dry grains of this population grown at different locations was determined using high performance liquid chromatography (HPLC). Subsequently, 175 polymorphic simple sequence repeat (SSR) markers were used to construct a linkage map with a total length of 4322.37 cM and with an average distance of 24.4 cM. A total of eight QTLs located on chromosomes 4, 5, 7, 9, and 10 were detected. The QTLs located in umc1632-umc1401 on chromosome 7 were detected in different environments and explained 11.28–20.25% of the phenotypic variation, implying it is the main QTL controlling zeaxanthin content in the dry grains of sweet corn. Collectively, the present study provides a genetic map and theoretical guidance for the cultivation of sweet corn varieties with a high zeaxanthin content. Full article
(This article belongs to the Special Issue Identification and Validation of Quantitative Trait Loci for Important Agronomic Traits in Food Crops)
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12 pages, 1623 KiB  
Article
Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan
by Yuliya Genievskaya, Alibek Zatybekov, Saule Abugalieva and Yerlan Turuspekov
Plants 2023, 12(12), 2375; https://doi.org/10.3390/plants12122375 - 19 Jun 2023
Cited by 3 | Viewed by 1418
Abstract
Barley (Hordeum vulgare L.) is one of the most produced cereal crops in the world. It has traditionally been used for the production of animal feed and for malting, as well as for human consumption. However, its production is highly affected by [...] Read more.
Barley (Hordeum vulgare L.) is one of the most produced cereal crops in the world. It has traditionally been used for the production of animal feed and for malting, as well as for human consumption. However, its production is highly affected by biotic stress factors, particularly the fungal pathogen Blumeria graminis (DC.) f. sp. hordei (Bgh), which causes powdery mildew (PM). In this study, a collection of 406 barley accessions from the USA, Kazakhstan, Europe, and Africa were assessed for resistance to PM over a 3-year period in southeastern Kazakhstan. The collection was grown in the field in 2020, 2021, and 2022 and was genotyped using the 9K SNP Illumina chip. A genome-wide association study (GWAS) was conducted to identify the quantitative trait loci (QTLs) associated with PM resistance. As a result, seven QTLs for PM resistance were detected on chromosomes 4H, 5H, and 7H (FDR p-values < 0.05). Genetic positions of two QTLs were similar to those of PM resistance QTLs previously reported in the scientific literature, suggesting that the five remaining QTLs are novel putative genetic factors for the studied trait. Haplotype analysis for seven QTLs revealed three haplotypes which were associated with total PM resistance and one haplotype associated with the high PM severity in the barley collection. Identified QTLs and haplotypes associated with the PM resistance of barley may be used for further analysis, trait pyramiding, and marker-assisted selection. Full article
(This article belongs to the Special Issue Identification and Validation of Quantitative Trait Loci for Important Agronomic Traits in Food Crops)
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13 pages, 1999 KiB  
Article
New Genes Identified as Modulating Salt Tolerance in Maize Seedlings Using the Combination of Transcriptome Analysis and BSA
by Yongxing Zhu, Ying Ren, Ji’an Liu, Wenguang Liang, Yuanyuan Zhang, Fengyuan Shen, Jiang Ling and Chunyi Zhang
Plants 2023, 12(6), 1331; https://doi.org/10.3390/plants12061331 - 15 Mar 2023
Cited by 7 | Viewed by 1972
Abstract
(1) Background: Salt stress is an abiotic factor that limits maize yield and quality. A highly salt-tolerance inbred AS5 and a salt-sensitive inbred NX420 collected from Ningxia Province, China, were used to identify new genes for modulating salt resistance in maize. (2) Methods: [...] Read more.
(1) Background: Salt stress is an abiotic factor that limits maize yield and quality. A highly salt-tolerance inbred AS5 and a salt-sensitive inbred NX420 collected from Ningxia Province, China, were used to identify new genes for modulating salt resistance in maize. (2) Methods: To understand the different molecular bases of salt tolerance in AS5 and NX420, we performed BSA-seq using an F2 population for two extreme bulks derived from the cross between AS5 and NX420. Transcriptomic analysis was also conducted for AS5 and NX420 at the seedling stage after treatment with 150 mM of NaCl for 14 days. (3) Results: AS5 had a higher biomass and lower Na+ content than NX420 in the seedling stage after treatment with 150 mM NaCl for 14 days. One hundred and six candidate regions for salt tolerance were mapped on all of the chromosomes through BSA-seq using F2 in an extreme population. Based on the polymorphisms identified between both parents, we detected 77 genes. A large number of differentially expressed genes (DEGs) at the seedling stage under salt stress between these two inbred lines were detected using transcriptome sequencing. GO analysis indicated that 925 and 686 genes were significantly enriched in the integral component of the membrane of AS5 and NX420, respectively. Among these results, two and four DEGs were identified as overlapping in these two inbred lines using BSA-seq and transcriptomic analysis, respectively. Two genes (Zm00001d053925 and Zm00001d037181) were detected in both AS5 and NX420; the transcription level of Zm00001d053925 was induced to be significantly higher in AS5 than in NX420 (41.99 times versus 6.06 times after 150 mM of NaCl treatment for 48 h), while the expression of Zm00001d037181 showed no significant difference upon salt treatment in both lines. The functional annotation of the new candidate genes showed that it was an unknown function protein. (4) Conclusions: Zm00001d053925 is a new functional gene responding to salt stress in the seedling stage, which provides an important genetic resource for salt-tolerant maize breeding. Full article
(This article belongs to the Special Issue Identification and Validation of Quantitative Trait Loci for Important Agronomic Traits in Food Crops)
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11 pages, 1498 KiB  
Communication
Genetic Basis of Resistance to Warrior (-) Yellow Rust Race at the Seedling Stage in Current Central and Northern European Winter Wheat Germplasm
by Fahimeh Shahinnia, Volker Mohler and Lorenz Hartl
Plants 2023, 12(3), 420; https://doi.org/10.3390/plants12030420 - 17 Jan 2023
Viewed by 2050
Abstract
To evaluate genetic variability and seedling plant response to a dominating Warrior (-) race of yellow rust in Northern and Central European germplasm, we used a population of 229 winter wheat cultivars and breeding lines for a genome-wide association study (GWAS). A wide [...] Read more.
To evaluate genetic variability and seedling plant response to a dominating Warrior (-) race of yellow rust in Northern and Central European germplasm, we used a population of 229 winter wheat cultivars and breeding lines for a genome-wide association study (GWAS). A wide variation in yellow rust disease severity (based on infection types 1–9) was observed in this panel. Four breeding lines, TS049 (from Austria), TS111, TS185, and TS229 (from Germany), and one cultivar, TS158 (KWS Talent), from Germany were found to be resistant to Warrior (-) FS 53/20 and Warrior (-) G 23/19. The GWAS identified five significant SNPs associated with yellow rust on chromosomes 1B, 2A, 5B, and 7A for Warrior (-) FS 53/20, while one SNP on chromosome 5B was associated with disease for Warrior (-) G 23/19. For Warrior (-) FS 53/20, we discovered a new QTL for yellow rust resistance associated with the marker Kukri_c5357_323 on chromosome 1B. The resistant alleles G and T at the marker loci Kukri_c5357_323 on chromosome 1B and Excalibur_c17489_804 on chromosome 5B showed the largest effects (1.21 and 0.81, respectively) on the severity of Warrior (-) FS 53/20 and Warrior (-) G 23/19. Our results provide the basis for knowledge-based resistance breeding in the face of the enormous impact of the Warrior (-) race on wheat production in Europe. Full article
(This article belongs to the Special Issue Identification and Validation of Quantitative Trait Loci for Important Agronomic Traits in Food Crops)
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19 pages, 1631 KiB  
Article
High-Density Linkage Mapping of Agronomic Trait QTLs in Wheat under Water Deficit Condition using Genotyping by Sequencing (GBS)
by Nayyer Abdollahi Sisi, Nils Stein, Axel Himmelbach and Seyed Abolghasem Mohammadi
Plants 2022, 11(19), 2533; https://doi.org/10.3390/plants11192533 - 27 Sep 2022
Cited by 4 | Viewed by 2227
Abstract
Improvement of grain yield is the ultimate goal for wheat breeding under water-limited environments. In the present study, a high-density linkage map was developed by using genotyping-by-sequencing (GBS) of a recombinant inbred line (RIL) population derived from the cross between Iranian landrace #49 [...] Read more.
Improvement of grain yield is the ultimate goal for wheat breeding under water-limited environments. In the present study, a high-density linkage map was developed by using genotyping-by-sequencing (GBS) of a recombinant inbred line (RIL) population derived from the cross between Iranian landrace #49 and cultivar Yecora Rojo. The population was evaluated in three locations in Iran during two years under irrigated and water deficit conditions for the agronomic traits grain yield (GY), plant height (PH), spike number per square meter (SM), 1000 kernel weight (TKW), grain number per spike (GNS), spike length (SL), biomass (BIO) and harvest index (HI). A linkage map was constructed using 5831 SNPs assigned to 21 chromosomes, spanning 3642.14 cM of the hexaploid wheat genome with an average marker density of 0.62 (markers/cM). In total, 85 QTLs were identified on 19 chromosomes (all except 5D and 6D) explaining 6.06–19.25% of the traits phenotypic variance. We could identify 20 novel QTLs explaining 8.87–19.18% of phenotypic variance on chromosomes 1A, 1B, 1D, 2B, 3A, 3B, 6A, 6B and 7A. For 35 out of 85 mapped QTLs functionally annotated genes were identified which could be related to a potential role in drought stress. Full article
(This article belongs to the Special Issue Identification and Validation of Quantitative Trait Loci for Important Agronomic Traits in Food Crops)
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20 pages, 5320 KiB  
Article
A GBS-Based GWAS Analysis of Leaf and Stripe Rust Resistance in Diverse Pre-Breeding Germplasm of Bread Wheat (Triticum aestivum L.)
by Kamran Saleem, Sajid Shokat, Muhammad Qandeel Waheed, Hafiz Muhammad Imran Arshad and Mian Abdur Rehman Arif
Plants 2022, 11(18), 2363; https://doi.org/10.3390/plants11182363 - 10 Sep 2022
Cited by 8 | Viewed by 2451
Abstract
Yellow (YR) and leaf (LR) rusts caused by Puccinia striiformis f. sp. tritici (Pst) and Puccinia triticina, respectively, are of utmost importance to wheat producers because of their qualitative and quantitative effect on yield. The search for new loci resistant to both [...] Read more.
Yellow (YR) and leaf (LR) rusts caused by Puccinia striiformis f. sp. tritici (Pst) and Puccinia triticina, respectively, are of utmost importance to wheat producers because of their qualitative and quantitative effect on yield. The search for new loci resistant to both rusts is an ongoing challenge faced by plant breeders and pathologists. Our investigation was conducted on a subset of 168 pre-breeding lines (PBLs) to identify the resistant germplasm against the prevalent local races of LR and YR under field conditions followed by its genetic mapping. Our analysis revealed a range of phenotypic responses towards both rusts. We identified 28 wheat lines with immune response and 85 resistant wheat genotypes against LR, whereas there were only eight immune and 52 resistant genotypes against YR. A GWAS (genome-wide association study) identified 190 marker-trait associations (MTAs), where 120 were specific to LR and 70 were specific to YR. These MTAs were confined to 86 quantitative trait loci (QTLs), where 50 QTLs carried MTAs associated with only LR, 29 QTLs carried MTAs associated with YR, and seven QTLs carried MTAs associated with both LR and YR. Possible candidate genes at the site of these QTLs are discussed. Overall, 70 PBLs carried all seven LR/YR QTLs. Furthermore, there were five PBLs with less than five scores for both LR and YR carrying positive alleles of all seven YR/LR QTLs, which are fit to be included in a breeding program for rust resistance induction. Full article
(This article belongs to the Special Issue Identification and Validation of Quantitative Trait Loci for Important Agronomic Traits in Food Crops)
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