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Molecular Genetics and Breeding Mechanisms in Crops

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 20418

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Guest Editor
College of Agriculture and Biotechnology, China Agricultural University, 2 Yuanmingyuan Xilu, Haidian District, Beijing 100193, China
Interests: molecular breeding; biotic and abiotic stress; molecular mechanism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the continuous progress of biotechnology, rapid development has been seen in molecular genetics and breeding theories, methods, as well as the creation of excellent germplasms. In order to promote academic exchange on the latest trends and achievements of molecular genetics and breeding in crops, this Special Issue will focus on molecular genetics and breeding mechanisms in crops with the aim of promoting the joint discussion of the latest research dynamics and directions and find opportunities for collaboration in this field. All original research papers and reviews are welcome for submission to this Special Issue.

Contributions in this Special Issue may include: studies on biological and abiotic stress resistance of crops, advances in crop genomics and proteomics, strategies for the combination of crop molecular breeding and conventional breeding, the and research and development of new technologies for crop germplasm innovation.

Prof. Dr. Shaozhen He
Guest Editor

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Keywords

  • molecular breeding
  • molecular genetics
  • germplasm
  • genomics
  • transcriptomics
  • proteomics
  • biological stress
  • abiotic stress
  • molecular mechanisms

Published Papers (10 papers)

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Research

24 pages, 9473 KiB  
Article
Genome-Wide Identification and Expression Analysis of ACTIN Family Genes in the Sweet Potato and Its Two Diploid Relatives
by Shuanghong Xia, Huan Zhang and Shaozhen He
Int. J. Mol. Sci. 2023, 24(13), 10930; https://doi.org/10.3390/ijms241310930 - 30 Jun 2023
Viewed by 1093
Abstract
ACTINs are structural proteins widely distributed in plants. They are the main components of microfilaments and participate in many crucial physiological activities, including the maintenance of cell shape and cytoplasmic streaming. Meanwhile, ACTIN, as a housekeeping gene, is widely used in qRT-PCR [...] Read more.
ACTINs are structural proteins widely distributed in plants. They are the main components of microfilaments and participate in many crucial physiological activities, including the maintenance of cell shape and cytoplasmic streaming. Meanwhile, ACTIN, as a housekeeping gene, is widely used in qRT-PCR analyses of plants. However, ACTIN family genes have not been explored in the sweet potato. In this study, we identified 30, 39, and 44 ACTINs in the cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively, via analysis of their genome structure and by phylogenetic characterization. These ACTINs were divided into six subgroups according to their phylogenetic relationships with Arabidopsis thaliana. The physiological properties of the protein, chromosome localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction networks, and expression patterns of these 113 ACTINs were systematically investigated. The results suggested that homologous ACTINs are differentiated in the sweet potato and its two diploid relatives, and play various vital roles in plant growth, tuberous root development, hormone crosstalk, and abiotic stress responses. Some stable ACTINs that could be used as internal reference genes were found in the sweet potato and its two diploid relatives, e.g., IbACTIN18, -20, and -16.2; ItfACTIN2.2, -16, and -10; ItbACTIN18 and -19.1. This work provides a comprehensive comparison and furthers our understanding of the ACTIN genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potatoes. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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23 pages, 10894 KiB  
Article
Genome-Wide Identification and Expression Analysis of SWEET Family Genes in Sweet Potato and Its Two Diploid Relatives
by Zhuoru Dai, Pengyu Yan, Shaozhen He, Licong Jia, Yannan Wang, Qingchang Liu, Hong Zhai, Ning Zhao, Shaopei Gao and Huan Zhang
Int. J. Mol. Sci. 2022, 23(24), 15848; https://doi.org/10.3390/ijms232415848 - 13 Dec 2022
Cited by 8 | Viewed by 1616
Abstract
Sugar Will Eventually be Exported Transporter (SWEET) proteins are key transporters in sugar transportation. They are involved in the regulation of plant growth and development, hormone crosstalk, and biotic and abiotic stress responses. However, SWEET family genes have not been explored in the [...] Read more.
Sugar Will Eventually be Exported Transporter (SWEET) proteins are key transporters in sugar transportation. They are involved in the regulation of plant growth and development, hormone crosstalk, and biotic and abiotic stress responses. However, SWEET family genes have not been explored in the sweet potato. In this study, we identified 27, 27, and 25 SWEETs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively. These SWEETs were divided into four subgroups according to their phylogenetic relationships with Arabidopsis. The protein physiological properties, chromosome localization, phylogenetic relationships, gene structures, promoter cis-elements, protein interaction networks, and expression patterns of these 79 SWEETs were systematically investigated. The results suggested that homologous SWEETs are differentiated in sweet potato and its two diploid relatives and play various vital roles in plant growth, tuberous root development, carotenoid accumulation, hormone crosstalk, and abiotic stress response. This work provides a comprehensive comparison and furthers our understanding of the SWEET genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potato. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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18 pages, 4488 KiB  
Article
Genomic Variation Underlying the Breeding Selection of Quinoa Varieties Longli-4 and CA3-1 in China
by Xiaofeng Li, Ruilan Ran, Guoxiong Chen and Pengshan Zhao
Int. J. Mol. Sci. 2022, 23(22), 14030; https://doi.org/10.3390/ijms232214030 - 14 Nov 2022
Cited by 4 | Viewed by 1189
Abstract
Quinoa (Chenopodium quinoa) is a well-known climate-resilient crop and has been introduced into multiple marginal lands across the world, including China, to improve food security and/or balanced nutrient supplies. Conventional breeding has been widely applied in the selection and breeding of [...] Read more.
Quinoa (Chenopodium quinoa) is a well-known climate-resilient crop and has been introduced into multiple marginal lands across the world, including China, to improve food security and/or balanced nutrient supplies. Conventional breeding has been widely applied in the selection and breeding of quinoa varieties in China since 1980s; however, few studies have been implemented on the genetic variances among different varieties developed by diversity breeding objectives. In this study, the phenotypic and genetic differences between two varieties (Longli-4 and CA3-1) from China were systematically analyzed. A total of 407,651 and 2,731,411 single nucleotide polymorphisms (SNPs) and 212,724 and 587,935 small insertion and deletion (INDELs) were detected for Longli-4 and CA3-1, respectively, when compared with the reference genome of PI614886. The SNPs/INDELs were unevenly distributed across each chromosome for both varieties. There were 143,996 SNPs and 83,410 INDELs shared between Longli-4 and CA3-1, accounting for 4% of the total variances. The variation was then screened based on the SNP effects. There were 818 and 73 genes with the variety-specific non-synonymous and stop-gain variation in Longli-4, whereas there were 13,701 and 733 genes in CA3-1. Specifically, 3501 genes with the non-synonymous variation and 74 genes with the stop-gain variation were found in both Longli-4 and CA3-1. These results suggest that convergent selection occurred during the different breeding processes. A set of candidate genes related to agronomic traits and domestication were further selected to detect the genetic divergence in detail in the two varieties. Only one domestication gene was identified having Longli-4-specific stop-gain variation. Twelve candidate genes related to betalain (1), flowering (4), seed size (2), domestication (1), and saponin (4) were identified having CA3-1-specific stop-gain variation. Interestingly, one seed size gene homologous of CKX1 (cytokinin oxidase/dehydrogenase 1) had the stop-gain variation in both varieties. This research will therefore provide guidance for the molecular-assisted breeding in quinoa. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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21 pages, 5756 KiB  
Article
Identifying Soybean Pod Borer (Leguminivora glycinivorella) Resistance QTLs and the Mechanism of Induced Defense Using Linkage Mapping and RNA-Seq Analysis
by Liangyu Chen, Baixing Song, Cheng Yu, Jun Zhang, Jian Zhang, Rui Bi, Xueying Li, Xiaobo Ren, Yanyu Zhu, Dan Yao, Yang Song, Songnan Yang and Rengui Zhao
Int. J. Mol. Sci. 2022, 23(18), 10910; https://doi.org/10.3390/ijms231810910 - 18 Sep 2022
Cited by 1 | Viewed by 1696
Abstract
The soybean pod borer (Leguminivora glycinivorella) (SPB) is a major cause of soybean (Glycine max L.) yield losses in northeast Asia, thus it is desirable to elucidate the resistance mechanisms involved in soybean response to the SPB. However, few studies [...] Read more.
The soybean pod borer (Leguminivora glycinivorella) (SPB) is a major cause of soybean (Glycine max L.) yield losses in northeast Asia, thus it is desirable to elucidate the resistance mechanisms involved in soybean response to the SPB. However, few studies have mapped SPB-resistant quantitative trait loci (QTLs) and deciphered the response mechanism in soybean. Here, we selected two soybean varieties, JY93 (SPB-resistant) and K6 (SPB-sensitive), to construct F2 and F2:3 populations for QTL mapping and collected pod shells before and after SPB larvae chewed on the two parents to perform RNA-Seq, which can identify stable QTLs and explore the response mechanism of soybean to the SPB. The results show that four QTLs underlying SPB damage to seeds were detected on chromosomes 4, 9, 13, and 15. Among them, qESP-9-1 was scanned in all environments, hence it can be considered a stable QTL. All QTLs explained 0.79 to 6.09% of the phenotypic variation. Meanwhile, 2298 and 3509 DEGs were identified for JY93 and K6, respectively, after the SPB attack, and most of these genes were upregulated. Gene Ontology enrichment results indicated that the SPB-induced and differently expressed genes in both parents are involved in biological processes such as wound response, signal transduction, immune response, and phytohormone pathways. Interestingly, secondary metabolic processes such as flavonoid synthesis were only significantly enriched in the upregulated genes of JY93 after SPB chewing compared with K6. Finally, we identified 18 candidate genes related to soybean pod borer resistance through the integration of QTL mapping and RNA-Seq analysis. Seven of these genes had similar expression patterns to the mapping parents in four additional soybean germplasm after feeding by the SPB. These results provide additional knowledge of the early response and induced defense mechanisms against the SPB in soybean, which could help in breeding SPB-resistant soybean accessions. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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15 pages, 3938 KiB  
Article
Uncovering Hierarchical Regulation among MYB-bHLH-WD40 Proteins and Manipulating Anthocyanin Pigmentation in Rice
by Xingming Sun, Zhanying Zhang, Jinjie Li, Hongliang Zhang, Youliang Peng and Zichao Li
Int. J. Mol. Sci. 2022, 23(15), 8203; https://doi.org/10.3390/ijms23158203 - 26 Jul 2022
Cited by 9 | Viewed by 1947
Abstract
Anthocyanins accumulate in various organs of rice, and the regulatory genes involved in pigmentation of specific organs, such as pericarp, hull, leaf, apiculus, and stigma have been elucidated. However, the corresponding gene for rice culm pigmentation has not been clarified. The well-known MYB-bHLH-WD40 [...] Read more.
Anthocyanins accumulate in various organs of rice, and the regulatory genes involved in pigmentation of specific organs, such as pericarp, hull, leaf, apiculus, and stigma have been elucidated. However, the corresponding gene for rice culm pigmentation has not been clarified. The well-known MYB-bHLH-WD40 (MBW) complex plays vital role in regulating the anthocyanin biosynthesis pathway in plants. However, the core members of MBW and the hierarchical regulation between these members are not fully elucidated in rice. Here, by map-based cloning, we identified the culm-specific pigmentation gene S1 whose alleles are also known for hull/pericarp pigmentation. We also clarified that one WD40 protein encoding gene, WA1, is indispensable for anthocyanin biosynthesis in rice. In the cascading regulation among MBW members, S1 (bHLH) acts as the master gene by activating the expression of C1 (MYB), and then C1 activates the expression of WA1 (WD40), which is unique in plant species. This enables MBW members to be coordinated in a common way to efficiently regulate anthocyanin biosynthesis genes. Based on these studies, we explored the minimal gene set required for anthocyanin biosynthesis in rice. These findings will help us design new rice varieties with anthocyanin accumulation in specific organs as needed. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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14 pages, 3943 KiB  
Article
Comprehensive Analysis for GRF Transcription Factors in Sacred Lotus (Nelumbo nucifera)
by Gui-Zhen Chen, Jie Huang, Xiao-Qin Zhou, Yang Hao, Jin-Liao Chen, Yu-Zhen Zhou, Sagheer Ahmad, Siren Lan, Zhong-Jian Liu and Dong-Hui Peng
Int. J. Mol. Sci. 2022, 23(12), 6673; https://doi.org/10.3390/ijms23126673 - 15 Jun 2022
Cited by 7 | Viewed by 2106
Abstract
Sacred lotus (Nelumbo nucifera) is an aquatic perennial plant with essential food, ornamental, and pharmacological value. Growth-regulating factor (GRF) is a transcription factor (TF) family that plays an important role in regulating the growth and development of plants. In this study, [...] Read more.
Sacred lotus (Nelumbo nucifera) is an aquatic perennial plant with essential food, ornamental, and pharmacological value. Growth-regulating factor (GRF) is a transcription factor (TF) family that plays an important role in regulating the growth and development of plants. In this study, a comprehensive analysis of the GRF family in N. nucifera was performed, and its role in N. nucifera development was studied. A total of eight GRF genes were identified in the N. nucifera genome. Phylogenetic analysis divided the 38 GRF genes into six clades, while the NuGRFs only contained five clades. The analyses of gene structures, motifs, and cis-acting regulatory elements of the GRF gene family were performed. In addition, the chromosome location and collinearity were analyzed. The expression pattern based on transcriptomic data and real-time reverse transcription-quantitative PCR (qRT-PCR) revealed that the GRF genes were expressed in multiple organs and were abundant in actively growing tissues, and the expression levels decreased as the age of N. nucifera increased. Then, 3D structures of the NuGRF proteins were predicted by homology modeling. Finally, the subcellular localization of GRF1 was ascertained in the tobacco leaf through a vector. Therefore, this study provides a comprehensive overview of the GRF TF family in N. nucifera. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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15 pages, 1731 KiB  
Article
Deciphering Pleiotropic Signatures of Regulatory SNPs in Zea mays L. Using Multi-Omics Data and Machine Learning Algorithms
by Ataul Haleem, Selina Klees, Armin Otto Schmitt and Mehmet Gültas
Int. J. Mol. Sci. 2022, 23(9), 5121; https://doi.org/10.3390/ijms23095121 - 04 May 2022
Cited by 2 | Viewed by 2181
Abstract
Maize is one of the most widely grown cereals in the world. However, to address the challenges in maize breeding arising from climatic anomalies, there is a need for developing novel strategies to harness the power of multi-omics technologies. In this regard, pleiotropy [...] Read more.
Maize is one of the most widely grown cereals in the world. However, to address the challenges in maize breeding arising from climatic anomalies, there is a need for developing novel strategies to harness the power of multi-omics technologies. In this regard, pleiotropy is an important genetic phenomenon that can be utilized to simultaneously enhance multiple agronomic phenotypes in maize. In addition to pleiotropy, another aspect is the consideration of the regulatory SNPs (rSNPs) that are likely to have causal effects in phenotypic development. By incorporating both aspects in our study, we performed a systematic analysis based on multi-omics data to reveal the novel pleiotropic signatures of rSNPs in a global maize population. For this purpose, we first applied Random Forests and then Markov clustering algorithms to decipher the pleiotropic signatures of rSNPs, based on which hierarchical network models are constructed to elucidate the complex interplay among transcription factors, rSNPs, and phenotypes. The results obtained in our study could help to understand the genetic programs orchestrating multiple phenotypes and thus could provide novel breeding targets for the simultaneous improvement of several agronomic traits. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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26 pages, 7883 KiB  
Article
Genome-Wide Identification and Characterization of CDPK Family Reveal Their Involvements in Growth and Development and Abiotic Stress in Sweet Potato and Its Two Diploid Relatives
by Xu Li, Limeng Zhao, Huan Zhang, Qingchang Liu, Hong Zhai, Ning Zhao, Shaopei Gao and Shaozhen He
Int. J. Mol. Sci. 2022, 23(6), 3088; https://doi.org/10.3390/ijms23063088 - 13 Mar 2022
Cited by 11 | Viewed by 2101
Abstract
Calcium-dependent protein kinase (CDPKs) is one of the calcium-sensing proteins in plants. They are likely to play important roles in growth and development and abiotic stress responses. However, these functions have not been explored in sweet potato. In this study, we identified 39 [...] Read more.
Calcium-dependent protein kinase (CDPKs) is one of the calcium-sensing proteins in plants. They are likely to play important roles in growth and development and abiotic stress responses. However, these functions have not been explored in sweet potato. In this study, we identified 39 CDPKs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), 35 CDPKs in diploid relative Ipomoea trifida (2n = 2x = 30), and 35 CDPKs in Ipomoea triloba (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological property, chromosome localization, phylogenetic relationship, gene structure, promoter cis-acting regulatory elements, and protein interaction network were systematically investigated to explore the possible roles of homologous CDPKs in the growth and development and abiotic stress responses of sweet potato. The expression profiles of the identified CDPKs in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting the difference in the evolutionary trajectories of hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato CDPK genes and provide more candidate genes for improving yield and abiotic stress tolerance in cultivated sweet potato. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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20 pages, 6032 KiB  
Article
Thidiazuron Promotes Leaf Abscission by Regulating the Crosstalk Complexities between Ethylene, Auxin, and Cytokinin in Cotton
by Fangjun Li, Qian Wu, Baopeng Liao, Keke Yu, Yini Huo, Lu Meng, Songman Wang, Baomin Wang, Mingwei Du, Xiaoli Tian and Zhaohu Li
Int. J. Mol. Sci. 2022, 23(5), 2696; https://doi.org/10.3390/ijms23052696 - 28 Feb 2022
Cited by 17 | Viewed by 2868
Abstract
Thidiazuron (TDZ) is widely used as a defoliant to induce leaf abscission in cotton. However, the underlying molecular mechanism is still unclear. In this study, RNA-seq and enzyme-linked immunosorbent assays (ELISA) were performed to reveal the dynamic transcriptome profiling and the change of [...] Read more.
Thidiazuron (TDZ) is widely used as a defoliant to induce leaf abscission in cotton. However, the underlying molecular mechanism is still unclear. In this study, RNA-seq and enzyme-linked immunosorbent assays (ELISA) were performed to reveal the dynamic transcriptome profiling and the change of endogenous phytohormones upon TDZ treatment in leaf, petiole, and abscission zone (AZ). We found that TDZ induced the gene expression of ethylene biosynthesis and signal, and promoted ethylene accumulation earlier in leaf than that in AZ. While TDZ down-regulated indole-3-acetic acid (IAA) biosynthesis genes mainly in leaf and IAA signal and transport genes. Furthermore, the IAA content reduced more sharply in the leaf than that in AZ to change the auxin gradient for abscission. TDZ suppressed CTK biosynthesis genes and induced CTK metabolic genes to reduce the IPA accumulation for the reduction of ethylene sensitivity. Furthermore, TDZ regulated the gene expression of abscisic acid (ABA) biosynthesis and signal and induced ABA accumulation between 12–48 h, which could up-regulate ABA response factor genes and inhibit IAA transporter genes. Our data suggest that TDZ orchestrates metabolism and signal of ethylene, auxin, and cytokinin, and also the transport of auxin in leaf, petiole, and AZ, to control leaf abscission. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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18 pages, 3103 KiB  
Article
Identification of Novel Genomic Regions for Bacterial Leaf Pustule (BLP) Resistance in Soybean (Glycine max L.) via Integrating Linkage Mapping and Association Analysis
by Fangzhou Zhao, Wei Cheng, Yanan Wang, Xuewen Gao, Debao Huang, Jiejie Kong, Augustine Antwi-Boasiako, Lingyi Zheng, Wenliang Yan, Fangguo Chang, Keke Kong, Ying-Yu Liao, Alejandra I. Huerta, Wusheng Liu, Mengchen Zhang and Tuanjie Zhao
Int. J. Mol. Sci. 2022, 23(4), 2113; https://doi.org/10.3390/ijms23042113 - 14 Feb 2022
Cited by 3 | Viewed by 2056
Abstract
Bacterial leaf pustule (BLP), caused by Xanthornonas axonopodis pv. glycines (Xag), is a worldwide disease of soybean, particularly in warm and humid regions. To date, little is known about the underlying molecular mechanisms of BLP resistance. The only single recessive resistance gene rxp [...] Read more.
Bacterial leaf pustule (BLP), caused by Xanthornonas axonopodis pv. glycines (Xag), is a worldwide disease of soybean, particularly in warm and humid regions. To date, little is known about the underlying molecular mechanisms of BLP resistance. The only single recessive resistance gene rxp has not been functionally identified yet, even though the genotypes carrying the gene have been widely used for BLP resistance breeding. Using a linkage mapping in a recombinant inbred line (RIL) population against the Xag strain Chinese C5, we identified that quantitative trait locus (QTL) qrxp–17–2 accounted for 74.33% of the total phenotypic variations. We also identified two minor QTLs, qrxp–05–1 and qrxp–17–1, that accounted for 7.26% and 22.26% of the total phenotypic variations, respectively, for the first time. Using a genome-wide association study (GWAS) in 476 cultivars of a soybean breeding germplasm population, we identified a total of 38 quantitative trait nucleotides (QTNs) on chromosomes (Chr) 5, 7, 8, 9,15, 17, 19, and 20 under artificial infection with C5, and 34 QTNs on Chr 4, 5, 6, 9, 13, 16, 17, 18, and 20 under natural morbidity condition. Taken together, three QTLs and 11 stable QTNs were detected in both linkage mapping and GWAS analysis, and located in three genomic regions with the major genomic region containing qrxp_17_2. Real-time RT-PCR analysis of the relative expression levels of five potential candidate genes in the resistant soybean cultivar W82 following Xag treatment showed that of Glyma.17G086300, which is located in qrxp–17–2, significantly increased in W82 at 24 and 72 h post-inoculation (hpi) when compared to that in the susceptible cultivar Jack. These results indicate that Glyma.17G086300 is a potential candidate gene for rxp and the QTLs and QTNs identified in this study will be useful for marker development for the breeding of Xag-resistant soybean cultivars. Full article
(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops)
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