Crop Genetics and Breeding

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 7119

Special Issue Editors

Special Issue Information

Dear Colleagues,

The journal Plants will be publishing a Special Issue on crop genetics and breeding. As an enduring and thriving academic discipline worldwide, crop genetics and breeding play crucial roles in agricultural development, contributing to the improvement of crop varieties with desirable traits such as higher yield and/or quality, resistance to biotic and abiotic stresses, tolerance to environmental stress, adaptability to climate change, enhanced nutritional content, etc. Great advances have been made in both theoretical and applied research fields of crop genetics and breeding and its linkages with related disciplines, attributing to advancements in genomics, biotechnology, molecular biology, population genetics, multi-omics, bioinformatics, etc., which have opened new interdisciplinary areas of plant genetics and breeding. We welcome submissions of different types of manuscripts, including original research papers, reviews and methods, encompassing, but not limited to:

  1. Genetic Diversity:
    - Genetic diversity is the foundation of crop improvement. It refers to the variety of genetic material within a species.
    - Maintaining and utilizing genetic diversity is essential for developing crops with resilience to changing environmental conditions.
  1. Gene Discovery:
    - Advances in molecular biology and genomics have facilitated the discovery and understanding of specific genes associated with important traits.
    - Identification of the genes responsible for traits such as drought tolerance, disease resistance and nutritional content allows for targeted breeding efforts.
  1. Marker-Assisted Selection (MAS):
    - MAS involves using molecular markers linked to specific genes or traits to aid in traditional breeding.
    - This technique allows for a more precise selection of desired traits and reduces the time needed for conventional breeding.
  1. Genome Editing:
    - Technologies such as CRISPR-Cas9 have revolutionized genetic engineering by enabling the precise modification of specific genes.
    - Genome editing can be used to enhance traits or introduce new traits into crops more rapidly than traditional breeding methods.
  1. Quantitative Genetics:
    - Quantitative genetics involves the study of traits that are controlled by multiple genes, often with a significant environmental influence.|
    - Understanding the genetic basis of quantitative traits helps breeders make more informed decisions in selecting plants for breeding programs.
  1. Hybridization and Crossbreeding:
    - Crossbreeding involves mating individuals from different populations to combine desirable traits from each parent.
    - Hybrid varieties often exhibit heterosis or hybrid vigor, resulting in superior performance compared to their parents.
  1. Genetic Modification (GM):
    - Genetic modification involves the introduction of genes from different organisms to confer specific traits.
    - GM crops may have improved resistance to pests, diseases or environmental stresses.
  1. Phenotypic Selection:
    - Traditional breeding methods often rely on the observation of physical characteristics (phenotypes) to select plants with desired traits.
    - This method has been used for centuries and remains an important part of many breeding programs.
  1. Data-Driven Breeding:
    - With the advent of big data and bioinformatics, there is an increasing emphasis on data-driven approaches in crop breeding.
    - Analyzing large datasets can help identify patterns, correlations, and markers associated with desirable traits.

Prof. Dr. Hai Du
Dr. Zhe Liang
Guest Editors

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Keywords

  • crops
  • population
  • QTL
  • sequencing
  • genome
  • SNP
  • molecular markers
  • genome editing
  • phenotypes
  • omics
  • polyploidy
  • evolution

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Published Papers (6 papers)

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Research

15 pages, 2501 KiB  
Article
Genome-Wide Characterization of Alfin-like Genes in Brassica napus and Functional Analyses of BnaAL02 and BnaAL28 in Response to Nitrogen and Phosphorus Deficiency
by Zexuan Wu, Shiying Liu, Xinyun Zhang, Xingzhi Qian, Zhuo Chen, Huiyan Zhao, Huafang Wan, Nengwen Yin, Jiana Li, Cunmin Qu and Hai Du
Plants 2024, 13(17), 2493; https://doi.org/10.3390/plants13172493 - 5 Sep 2024
Viewed by 670
Abstract
Alfin-like proteins (ALs) form a plant-specific transcription factor (TF) gene family involved in the regulation of plant growth and development, and abiotic stress response. In this study, 30 ALs were identified in Brassica napus ecotype ‘Zhongshuang 11’ genome (BnaALs), and unevenly distributed on [...] Read more.
Alfin-like proteins (ALs) form a plant-specific transcription factor (TF) gene family involved in the regulation of plant growth and development, and abiotic stress response. In this study, 30 ALs were identified in Brassica napus ecotype ‘Zhongshuang 11’ genome (BnaALs), and unevenly distributed on 15 chromosomes. Structural characteristic analysis showed that all of the BnaALs contained two highly conserved domains: the N terminal DUF3594 domain and the C-terminal PHD-finger domain. The BnaALs were classified into four groups (Group I-IV), supported by conserved intron–exon and protein motif structures in each group. The allopolyploid event between B. oleracea and B. rapa ancestors and the small-scale duplication events in B. napus both contributed to the large BnaALs expansion. The promoter regions of BnaALs contained multiple abiotic stress cis-elements. The BnaALs in I-IV groups were mainly expressed in cotyledon, petal, root, silique, and seed tissues, and the duplicated gene pairs shared highly similar expression patterns. RNA-seq and RT-qPCR analysis showed that BnaALs were obviously induced by low nitrogen (LN) and low phosphorus (LP) treatments in roots. Overexpressing BnaAL02 and BnaAL28 in Arabidopsis demonstrated their functions in response to LN and LP stresses. BnaAL28 enhanced primary roots’ (PRs) length and lateral roots’ (LRs) number under LP and LN conditions, where BnaAL02 can inhibit LR numbers under the two conditions. They can promote root hair (RH) elongation under LP conditions; however, they suppressed RH elongation under LN conditions. Our result provides new insight into the functional dissection of this family in response to nutrient stresses in plants. Full article
(This article belongs to the Special Issue Crop Genetics and Breeding)
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13 pages, 4971 KiB  
Article
Stigma and Glume Characteristics Synergistically Determine the Stigma Exsertion Rate in Thermo-Photo-Sensitive Genic Male Sterile Wheat
by Hongsheng Li, Zhonghui Yang, Shaoxiang Li, Ahmed M. S. Elfanah, Sedhom Abdelkhalik, Xiong Tang, Jian Yin, Mingliang Ding, Kun Liu, Mujun Yang and Xiue Wang
Plants 2024, 13(16), 2267; https://doi.org/10.3390/plants13162267 - 15 Aug 2024
Viewed by 588
Abstract
Wheat hybrids have been widely demonstrated to have remarkable heterosis or hybrid vigor in increasing yield potential and stability since the 1960s. Two-line hybrid wheat can achieve higher yields than local varieties, especially in marginal environments. However, the commercial application of hybrid wheat [...] Read more.
Wheat hybrids have been widely demonstrated to have remarkable heterosis or hybrid vigor in increasing yield potential and stability since the 1960s. Two-line hybrid wheat can achieve higher yields than local varieties, especially in marginal environments. However, the commercial application of hybrid wheat is hindered by higher seed costs, primarily due to lower yields in hybrid seed production. Stigma exsertion has been verified as a decisive factor in increasing rice’s hybrid seed yield, but more investigation is needed in hybrid wheat breeding and production. In this study, four thermo-photo-sensitive genic male sterile lines, including K41S, K64S, K66S, and K68S, with different stigma exsertion rates (SERs) were used to compare the differences in floral architecture relative to stigma exsertion over two growing seasons. The results revealed that the K41S and K64S exhibited a relatively higher SER at 21.87% and 22.81%, respectively. No exserted stigma was observed in K66S, and K68S had an SER of only 0.82%. This study found that the stigma length, glume width and the length–width ratio of the glume were significantly correlated with the SER, with correlation coefficients of 0.46, −0.46 and 0.60, respectively. Other stigma features such as the branch angle, stretch width and hairbrush length, as well as the glume length, also had a weakly positive correlation with SER (r = 0.09–0.27). For K41S and K64S, the SER was significantly affected by the differences in the stigma branch angle and stigma stretch width among florets. A cross-pollination survey showed that the out-crossing ability of florets with an exserted stigma was about three times as high as that of florets with a non-exserted stigma. As a result, the stigma-exserted florets that accounted for 21.87% and 22.81% of the total florets in K41S and K64S produced 46.80% and 48.53% of the total cross-pollinated seeds in both sterile lines. These findings suggest that a longer stigma combined with a slender glume appears to be the essential floral feature of stigma exsertion in sterile wheat lines. It is expected that breeding and utilizing sterile lines with a higher SER would be a promising solution to cost-effective hybrid wheat seed production. Full article
(This article belongs to the Special Issue Crop Genetics and Breeding)
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15 pages, 3661 KiB  
Article
Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize (Zea mays L.)
by Jin Yang, Zhou Liu, Yanbo Liu, Xiujun Fan, Lei Gao, Yangping Li, Yufeng Hu, Kun Hu and Yubi Huang
Plants 2024, 13(11), 1533; https://doi.org/10.3390/plants13111533 - 1 Jun 2024
Viewed by 970
Abstract
Deep sowing is an efficient strategy for maize to ensure the seedling emergence rate under adverse conditions such as drought or low temperatures. However, the genetic basis of deep-sowing tolerance-related traits in maize remains largely unknown. In this study, we performed a genome-wide [...] Read more.
Deep sowing is an efficient strategy for maize to ensure the seedling emergence rate under adverse conditions such as drought or low temperatures. However, the genetic basis of deep-sowing tolerance-related traits in maize remains largely unknown. In this study, we performed a genome-wide association study on traits related to deep-sowing tolerance, including mesocotyl length (ML), coleoptile length (CL), plumule length (PL), shoot length (SL), and primary root length (PRL), using 255 maize inbred lines grown in three different environments. We identified 23, 6, 4, and 4 quantitative trait loci (QTLs) associated with ML, CL, PL, and SL, respectively. By analyzing candidate genes within these QTLs, we found a γ-tubulin-containing complex protein, ZmGCP2, which was significantly associated with ML, PL, and SL. Loss of function of ZmGCP2 resulted in decreased PL, possibly by affecting the cell elongation, thus affecting SL. Additionally, we identified superior haplotypes and allelic variations of ZmGCP2 with a longer PL and SL, which may be useful for breeding varieties with deep-sowing tolerance to improve maize cultivation. Full article
(This article belongs to the Special Issue Crop Genetics and Breeding)
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14 pages, 6991 KiB  
Article
Comparative Genomics of Lotus japonicus Reveals Insights into Proanthocyanidin Accumulation and Abiotic Stress Response
by Zhanmin Sun, Ziyang Liu, Manqing Zhi, Qifan Ran, Wenbo Xue, Yixiong Tang and Yanmin Wu
Plants 2024, 13(8), 1151; https://doi.org/10.3390/plants13081151 - 20 Apr 2024
Viewed by 1010
Abstract
Lotus japonicus, is an important perennial model legume, has been widely used for studying biological processes such as symbiotic nitrogen fixation, proanthocyanidin (PA) biosynthesis, and abiotic stress response. High-quality L. japonicus genomes have been reported recently; however, the genetic basis of genes [...] Read more.
Lotus japonicus, is an important perennial model legume, has been widely used for studying biological processes such as symbiotic nitrogen fixation, proanthocyanidin (PA) biosynthesis, and abiotic stress response. High-quality L. japonicus genomes have been reported recently; however, the genetic basis of genes associated with specific characters including proanthocyanidin distribution in most tissues and tolerance to stress has not been systematically explored yet. Here, based on our previous high-quality L. japonicus genome assembly and annotation, we compared the L. japonicus MG-20 genome with those of other legume species. We revealed the expansive and specific gene families enriched in secondary metabolite biosynthesis and the detection of external stimuli. We suggested that increased copy numbers and transcription of PA-related genes contribute to PA accumulation in the stem, petiole, flower, pod, and seed coat of L. japonicus. Meanwhile, According to shared and unique transcription factors responding to five abiotic stresses, we revealed that MYB and AP2/ERF play more crucial roles in abiotic stresses. Our study provides new insights into the key agricultural traits of L. japonicus including PA biosynthesis and response to abiotic stress. This may provide valuable gene resources for legume forage abiotic stress resistance and nutrient improvement. Full article
(This article belongs to the Special Issue Crop Genetics and Breeding)
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14 pages, 2774 KiB  
Article
Transcriptomic Analysis of Self-Incompatibility in Alfalfa
by Lulu Li, Sinan Liu, Yulu Wang, Yangzhou Shang, Zhi Qi, Hao Lin and Lifang Niu
Plants 2024, 13(6), 875; https://doi.org/10.3390/plants13060875 - 19 Mar 2024
Viewed by 1328
Abstract
Alfalfa (Medicago sativa L.) is an important forage crop worldwide, but molecular genetics and breeding research in this species are hindered by its self-incompatibility (SI). Although the mechanisms underlying SI have been extensively studied in other plant families, SI in legumes, including [...] Read more.
Alfalfa (Medicago sativa L.) is an important forage crop worldwide, but molecular genetics and breeding research in this species are hindered by its self-incompatibility (SI). Although the mechanisms underlying SI have been extensively studied in other plant families, SI in legumes, including alfalfa, remains poorly understood. Here, we determined that self-pollinated pollen tubes could germinate on the stigma of alfalfa, grow through the style, and reach the ovarian cavity, but the ovules collapsed ~48 h after self-pollination. A transcriptomic analysis of dissected pistils 24 h after self-pollination identified 941 differently expressed genes (DEGs), including 784 upregulated and 157 downregulated genes. A gene ontology (GO) analysis showed that the DEGs were highly enriched in functions associated with the regulation of pollen tube growth and pollen germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that pentose and glucuronate interconversion, plant hormone signal transduction, the spliceosome, and ribosomes might play important roles in SI. Our co-expression analysis showed that F-box proteins, serine/threonine protein kinases, calcium-dependent protein kinases (CDPKs), bHLHs, bZIPs, and MYB-related family proteins were likely involved in the SI response. Our study provides a catalog of candidate genes for further study to understand SI in alfalfa and related legumes. Full article
(This article belongs to the Special Issue Crop Genetics and Breeding)
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18 pages, 3188 KiB  
Article
Transcriptome Profiling Reveals the Gene Network Responding to Low Nitrogen Stress in Wheat
by Yiwei Wang, Pengfeng Li, Yiwang Zhu, Yuping Shang, Zhiqiang Wu, Yongfu Tao, Hongru Wang, Dongxi Li and Cuijun Zhang
Plants 2024, 13(3), 371; https://doi.org/10.3390/plants13030371 - 26 Jan 2024
Cited by 1 | Viewed by 1600
Abstract
As one of the essential nutrients for plants, nitrogen (N) has a major impact on the yield and quality of wheat worldwide. Due to chemical fertilizer pollution, it has become increasingly important to improve crop yield by increasing N use efficiency (NUE). Therefore, [...] Read more.
As one of the essential nutrients for plants, nitrogen (N) has a major impact on the yield and quality of wheat worldwide. Due to chemical fertilizer pollution, it has become increasingly important to improve crop yield by increasing N use efficiency (NUE). Therefore, understanding the response mechanisms to low N (LN) stress is essential for the regulation of NUE in wheat. In this study, LN stress significantly accelerated wheat root growth, but inhibited shoot growth. Further transcriptome analysis showed that 8468 differentially expressed genes (DEGs) responded to LN stress. The roots and shoots displayed opposite response patterns, of which the majority of DEGs in roots were up-regulated (66.15%; 2955/4467), but the majority of DEGs in shoots were down-regulated (71.62%; 3274/4565). GO and KEGG analyses showed that nitrate reductase activity, nitrate assimilation, and N metabolism were significantly enriched in both the roots and shoots. Transcription factor (TF) and protein kinase analysis showed that genes such as MYB-related (38/38 genes) may function in a tissue-specific manner to respond to LN stress. Moreover, 20 out of 107 N signaling homologous genes were differentially expressed in wheat. A total of 47 transcriptome datasets were used for weighted gene co-expression network analysis (17,840 genes), and five TFs were identified as the potential hub regulatory genes involved in the response to LN stress in wheat. Our findings provide insight into the functional mechanisms in response to LN stress and five candidate regulatory genes in wheat. These results will provide a basis for further research on promoting NUE in wheat. Full article
(This article belongs to the Special Issue Crop Genetics and Breeding)
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