International Journal of Molecular Sciences

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11 pages, 1652 KiB

Open AccessArticle

Teosinte-Derived Advanced Backcross Population Harbors Genomic Regions for Grain Yield Attributing Traits in Maize

by Pardeep Kumar, Mukesh Choudhary, Seema Sheoran, Ningthai Longmei, Bhupender Kumar, Bahadur Singh Jat, Manesh Chander Dagla, Bharat Bhushan, Sumit Kumar Aggarwal, Pravin Kumar Bagaria, Ankush Sharma and Shyam Bir Singh

Int. J. Mol. Sci. 2024, 25(19), 10300; https://doi.org/10.3390/ijms251910300 - 25 Sep 2024

Viewed by 325

Abstract

Maize is a highly versatile crop holding significant importance in global food, feed and nutritional security. Grain yield is a complex trait and difficult to improve without targeting the improvement of grain yield attributing traits, which are relatively less complex in nature. Hence, [...] Read more.

Maize is a highly versatile crop holding significant importance in global food, feed and nutritional security. Grain yield is a complex trait and difficult to improve without targeting the improvement of grain yield attributing traits, which are relatively less complex in nature. Hence, considering the erosion in genetic diversity, there is an urgent need to use wild relatives for genetic diversification and unravel the genomic regions for grain yield attributing traits in maize. Thus, the current study aimed to identify quantitative trait loci (QTLs) linked with grain yield and yield attributing traits. Two BC₂F₂ populations developed from the cross of LM13 with Zea parviglumis (population 1) and LM14 with Zea parviglumis (population 2) were genotyped and phenotyped in field conditions in the kharif season. BC₂F_2:3 lines in both populations were phenotyped again for grain yield and attributing traits in the spring season. In total, three QTLs each for ear height (EH), two QTLs for flag leaf length (FLL) and one QTL each for ear diameter (ED), plant height, flag leaf length (FLL), flag leaf width and 100 kernel-weight were identified in population 1. In population 2, two QTLs for kernel row per ear (KRPE) and one QTL for FLL were detected in. QTLs for EH, FLL and KPRE showed consistency across seasons. Among the identified QTLs, six QTLs were found to be co-localized near identified genomic regions in previous studies, validating their potential in contributing to trait expression. The identified QTLs can be utilized for marker assisted selection, transferring favorable alleles from wild relatives in modern maize. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops: 2nd Edition)

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11 pages, 2175 KiB

Open AccessArticle

Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy in Wheat

by Yu Gao, Linyi Qiao, Chao Mei, Lina Nong, Qiqi Li, Xiaojun Zhang, Rui Li, Wei Gao, Fang Chen, Lifang Chang, Shuwei Zhang, Huijuan Guo, Tianling Cheng, Huiqin Wen, Zhijian Chang and Xin Li

Int. J. Mol. Sci. 2024, 25(7), 3681; https://doi.org/10.3390/ijms25073681 - 26 Mar 2024

Viewed by 940

Abstract

The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain [...] Read more.

The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops: 2nd Edition)

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22 pages, 1993 KiB

Open AccessArticle

Construction of Genetic Map and QTL Mapping for Seed Size and Quality Traits in Soybean (Glycine max L.)

by Weiran Gao, Ronghan Ma, Xi Li, Jiaqi Liu, Aohua Jiang, Pingting Tan, Guoxi Xiong, Chengzhang Du, Jijun Zhang, Xiaochun Zhang, Xiaomei Fang, Zelin Yi and Jian Zhang

Int. J. Mol. Sci. 2024, 25(5), 2857; https://doi.org/10.3390/ijms25052857 - 1 Mar 2024

Cited by 3 | Viewed by 1460

Abstract

Soybean (Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Soybean yield and quality traits are mostly quantitative traits controlled by multiple genes. [...] Read more.

Soybean (Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Soybean yield and quality traits are mostly quantitative traits controlled by multiple genes. The quantitative trait loci (QTL) mapping for yield and quality traits, as well as for the identification of mining-related candidate genes, is of great significance for the molecular breeding and understanding the genetic mechanism. In this study, 186 individual plants of the F₂ generation derived from crosses between Changjiangchun 2 and Yushuxian 2 were selected as the mapping population to construct a molecular genetic linkage map. A genetic map containing 445 SSR markers with an average distance of 5.3 cM and a total length of 2375.6 cM was obtained. Based on constructed genetic map, 11 traits including hundred-seed weight (HSW), seed length (SL), seed width (SW), seed length-to-width ratio (SLW), oil content (OIL), protein content (PRO), oleic acid (OA), linoleic acid (LA), linolenic acid (LNA), palmitic acid (PA), stearic acid (SA) of yield and quality were detected by the multiple- d size traits and 113 QTLs related to quality were detected by the multiple QTL model (MQM) mapping method across generations F₂, F_2:3, F_2:4, and F_2:5. A total of 71 QTLs related to seed size traits and 113 QTLs related to quality traits were obtained in four generations. With those QTLs, 19 clusters for seed size traits and 20 QTL clusters for quality traits were summarized. Two promising clusters, one related to seed size traits and the other to quality traits, have been identified. The cluster associated with seed size traits spans from position 27876712 to 29009783 on Chromosome 16, while the cluster linked to quality traits spans from position 12575403 to 13875138 on Chromosome 6. Within these intervals, a reference genome of William82 was used for gene searching. A total of 36 candidate genes that may be involved in the regulation of soybean seed size and quality were screened by gene functional annotation and GO enrichment analysis. The results will lay the theoretical and technical foundation for molecularly assisted breeding in soybean. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops: 2nd Edition)

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20 pages, 5167 KiB

Open AccessArticle

IbMYC2 Contributes to Salt and Drought Stress Tolerance via Modulating Anthocyanin Accumulation and ROS-Scavenging System in Sweet Potato

by Yuanfeng Hu, Hongyuan Zhao, Luyao Xue, Nan Nie, Huan Zhang, Ning Zhao, Shaozhen He, Qingchang Liu, Shaopei Gao and Hong Zhai

Int. J. Mol. Sci. 2024, 25(4), 2096; https://doi.org/10.3390/ijms25042096 - 8 Feb 2024

Cited by 4 | Viewed by 1592

Abstract

Basic helix–loop–helix (bHLH) transcription factors extensively affect various physiological processes in plant metabolism, growth, and abiotic stress. However, the regulation mechanism of bHLH transcription factors in balancing anthocyanin biosynthesis and abiotic stress in sweet potato (Ipomoea batata (L.) Lam.) remains unclear. Previously, [...] Read more.

Basic helix–loop–helix (bHLH) transcription factors extensively affect various physiological processes in plant metabolism, growth, and abiotic stress. However, the regulation mechanism of bHLH transcription factors in balancing anthocyanin biosynthesis and abiotic stress in sweet potato (Ipomoea batata (L.) Lam.) remains unclear. Previously, transcriptome analysis revealed the genes that were differentially expressed among the purple-fleshed sweet potato cultivar ‘Jingshu 6’ and its anthocyanin-rich mutant ‘JS6-5’. Here, we selected one of these potential genes, IbMYC2, which belongs to the bHLH transcription factor family, for subsequent analyses. The expression of IbMYC2 in the JS6-5 storage roots is almost four-fold higher than Jingshu 6 and significantly induced by hydrogen peroxide (H₂O₂), methyl jasmonate (MeJA), NaCl, and polyethylene glycol (PEG)6000. Overexpression of IbMYC2 significantly enhances anthocyanin production and exhibits a certain antioxidant capacity, thereby improving salt and drought tolerance. In contrast, reducing IbMYC2 expression increases its susceptibility. Our data showed that IbMYC2 could elevate the expression of anthocyanin synthesis pathway genes by binding to IbCHI and IbDFR promoters. Additionally, overexpressing IbMYC2 activates genes encoding reactive oxygen species (ROS)-scavenging and proline synthesis enzymes under salt and drought conditions. Taken together, these results demonstrate that the IbMYC2 gene exercises a significant impact on crop quality and stress resistance. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops: 2nd Edition)

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13 pages, 5352 KiB

Open AccessArticle

Identification of a Branch Number Locus in Soybean Using BSA-Seq and GWAS Approaches

by Dongqing Dai, Lu Huang, Xiaoyan Zhang, Shiqi Zhang, Yuting Yuan, Gufeng Wu, Yichen Hou, Xingxing Yuan, Xin Chen and Chenchen Xue

Int. J. Mol. Sci. 2024, 25(2), 873; https://doi.org/10.3390/ijms25020873 - 10 Jan 2024

Cited by 3 | Viewed by 1267

Abstract

The determination of the soybean branch number plays a pivotal role in plant morphogenesis and yield components. This polygenic trait is subject to environmental influences, and despite its significance, the genetic mechanisms governing the soybean branching number remain incompletely understood. To unravel these [...] Read more.

The determination of the soybean branch number plays a pivotal role in plant morphogenesis and yield components. This polygenic trait is subject to environmental influences, and despite its significance, the genetic mechanisms governing the soybean branching number remain incompletely understood. To unravel these mechanisms, we conducted a comprehensive investigation employing a genome-wide association study (GWAS) and bulked sample analysis (BSA). The GWAS revealed 18 SNPs associated with the soybean branch number, among which qGBN3 on chromosome 2 emerged as a consistently detected locus across two years, utilizing different models. In parallel, a BSA was executed using an F₂ population derived from contrasting cultivars, Wandou35 (low branching number) and Ruidou1 (high branching number). The BSA results pinpointed a significant quantitative trait locus (QTL), designated as qBBN1, located on chromosome 2 by four distinct methods. Importantly, both the GWAS and BSA methods concurred in co-locating qGBN3 and qBBN1. In the co-located region, 15 candidate genes were identified. Through gene annotation and RT-qPCR analysis, we predicted that Glyma.02G125200 and Glyma.02G125600 are candidate genes regulating the soybean branch number. These findings significantly enhance our comprehension of the genetic intricacies regulating the branch number in soybeans, offering promising candidate genes and materials for subsequent investigations aimed at augmenting the soybean yield. This research represents a crucial step toward unlocking the full potential of soybean cultivation through targeted genetic interventions. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops: 2nd Edition)

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13 pages, 4101 KiB

Open AccessArticle

GmCBP60b Plays Both Positive and Negative Roles in Plant Immunity

by Mei-Yan Ye, Hu-Jiao Lan and Jian-Zhong Liu

Int. J. Mol. Sci. 2024, 25(1), 378; https://doi.org/10.3390/ijms25010378 - 27 Dec 2023

Cited by 3 | Viewed by 1104

Abstract

CBP60b (CALMODULIN-BINDING PROTEIN 60b) is a member of the CBP60 transcription factor family. In Arabidopsis, AtCBP60b not only regulates growth and development but also activates the transcriptions in immune responses. So far, CBP60b has only been studied extensively in the model plant [...] Read more.

CBP60b (CALMODULIN-BINDING PROTEIN 60b) is a member of the CBP60 transcription factor family. In Arabidopsis, AtCBP60b not only regulates growth and development but also activates the transcriptions in immune responses. So far, CBP60b has only been studied extensively in the model plant Arabidopsis and rarely in crops. In this study, Bean pod mottle virus (BPMV)-mediated gene silencing (BPMV-VIGS) was used to silence GmCBP60b.1/2 in soybean plants. The silencing of GmCBP60b.1/2 resulted in typical autoimmunity, such as dwarfism and enhanced resistance to both Soybean mosaic virus (SMV) and Pseudomonas syringae pv. glycinea (Psg). To further understand the roles of GmCBP60b in immunity and circumvent the recalcitrance of soybean transformation, we generated transgenic tobacco lines that overexpress GmCBP60b.1. The overexpression of GmCBP60b.1 also resulted in autoimmunity, including spontaneous cell death on the leaves, highly induced expression of PATHOGENESIS-RELATED (PR) genes, significantly elevated accumulation of defense hormone salicylic acid (SA), and significantly enhanced resistance to Pst DC3000 (Pseudomonas syrangae pv. tomato DC3000). The transient coexpression of a luciferase reporter gene driven by the promoter of soybean SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (GmSARD1) (ProGmSARD1::LUC), together with GmCBP60b.1 driven by the 35S promoter, led to the activation of the LUC reporter gene, suggesting that GmCBP60b.1 could bind to the core (A/T)AATT motifs within the promoter region of GmSARD1 and, thus, activate the expression of the LUC reporter. Taken together, our results indicate that GmCBP60b.1/2 play both positive and negative regulatory roles in immune responses. These results also suggest that the function of CBP60b is conserved across plant species. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops: 2nd Edition)

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13 pages, 2727 KiB

Open AccessArticle

Silencing GmATG7 Leads to Accelerated Senescence and Enhanced Disease Resistance in Soybean

by Said M. Hashimi, Min-Jun Huang, Mohammad Q. Amini, Wen-Xu Wang, Tian-Yao Liu, Yu Chen, Li-Na Liao, Hu-Jiao Lan and Jian-Zhong Liu

Int. J. Mol. Sci. 2023, 24(22), 16508; https://doi.org/10.3390/ijms242216508 - 20 Nov 2023

Cited by 1 | Viewed by 1211

Abstract

Autophagy plays a critical role in nutrient recycling/re-utilizing under nutrient deprivation conditions. However, the role of autophagy in soybeans has not been intensively investigated. In this study, the Autophay-related gene 7 (ATG7) gene in soybeans (referred to as GmATG7) was [...] Read more.

Autophagy plays a critical role in nutrient recycling/re-utilizing under nutrient deprivation conditions. However, the role of autophagy in soybeans has not been intensively investigated. In this study, the Autophay-related gene 7 (ATG7) gene in soybeans (referred to as GmATG7) was silenced using a virus-induced gene silencing approach mediated by Bean pod mottle virus (BPMV). Our results showed that ATG8 proteins were highly accumulated in the dark-treated leaves of the GmATG7-silenced plants relative to the vector control leaves (BPMV-0), which is indicative of an impaired autophagy pathway. Consistent with the impaired autophagy, the dark-treated GmATG7-silenced leaves displayed an accelerated senescence phenotype, which was not seen on the dark-treated BPMV-0 leaves. In addition, the accumulation levels of both H₂O₂ and salicylic acid (SA) were significantly induced in the GmATG7-silenced plants compared with the BPMV-0 plants, indicating an activated immunity. Consistently, the GmATG7-silenced plants were more resistant against both Pseudomonas syringae pv. glycinea (Psg) and Soybean mosaic virus (SMV) compared with the BPMV-0 plants. However, the activated immunity in the GmATG7-silenced plant was not dependent upon the activation of MPK3/MPK6. Collectively, our results demonstrated that the function of GmATG7 is indispensable for autophagy in soybeans, and the activated immunity in the GmATG7-silenced plant is a result of impaired autophagy. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops: 2nd Edition)

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21 pages, 7617 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the Sucrose Synthase Gene Family in Sweet Potato and Its Two Diploid Relatives

by Zhicheng Jiang, Huan Zhang, Shaopei Gao, Hong Zhai, Shaozhen He, Ning Zhao and Qingchang Liu

Int. J. Mol. Sci. 2023, 24(15), 12493; https://doi.org/10.3390/ijms241512493 - 6 Aug 2023

Cited by 6 | Viewed by 1961

Abstract

Sucrose synthases (SUS; EC 2.4.1.13) encoded by a small multigene family are the central system of sucrose metabolism and have important implications for carbon allocation and energy conservation in nonphotosynthetic cells of plants. Though the SUS family genes (SUSs) have been [...] Read more.

Sucrose synthases (SUS; EC 2.4.1.13) encoded by a small multigene family are the central system of sucrose metabolism and have important implications for carbon allocation and energy conservation in nonphotosynthetic cells of plants. Though the SUS family genes (SUSs) have been identified in several plants, they have not been explored in sweet potato. In this research, nine, seven and seven SUSs were identified in the cultivated sweet potato (Ipomoea batatas, 2n = 6x = 90) as well as its two diploid wild relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30), respectively, and divided into three subgroups according to their phylogenetic relationships. Their protein physicochemical properties, chromosomal localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction network and expression patterns were systematically analyzed. The results indicated that the SUS gene family underwent segmental and tandem duplications during its evolution. The SUSs were highly expressed in sink organs. The IbSUSs especially IbSUS2, IbSUS5 and IbSUS7 might play vital roles in storage root development and starch biosynthesis. The SUSs could also respond to drought and salt stress responses and take part in hormone crosstalk. This work provides new insights for further understanding the functions of SUSs and candidate genes for improving yield, starch content, and abiotic stress tolerance in sweet potatoes. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Crops: 2nd Edition)

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