New Insights into Crop Molecular Breeding and Genetics

1. Introduction

As the global population continues to grow, the need to increase agricultural productivity is becoming increasingly urgent. Cultivation of crops are the basis of agricultural production, but traditional planting patterns have shortcomings, such as low yield, poor resistance to adversity, and weak resistance to diseases and pests. In order to solve these problems, researchers have begun to use biotechnologies such as gene editing, transgenic technology, molecular marker-assisted selection (MAS), genomics, and transcriptomics to optimize crops. This paper focuses on the latest discoveries of different crops published in agronomy regarding the regulation of plant developmental processes or agronomic traits, especially methods to increase crop yield, such as searching for elite genetic resources, adaptation to adversity stress, improvement of crop resistance to pests and diseases, and the potential utilization of biotechnology in the genetic improvement of crops.

2. Research in Food Crops

2.1. Research in Rice

Rice is one of the world’s major food crops and is used as a major source of energy by more than 3 billion people worldwide, accounting for 25% of the world’s total caloric intake [1]. In recent years, rice yield has increased dramatically with the improvement of hybridization technology and cultivation management, but it is still difficult to meet the growing demand of the population [2]. Therefore, most of the current rice breeders concentrate their efforts on seeking various methods, such as gene editing, MAS, and genomics, to improve rice yield. Rice yield is associated with a variety of traits, among which the defining trait is grain filling, and the development of rice grains during filling directly affects rice fruiting rate and grain weight. Lee et al. [3] identified three quantitative trait loci (QTLs), qFG3, qFG5-1, and qFG5-2, significantly associated with the control of grain filling by a doubled haploid rice population, of which qFG3 is a novel and stable QTL that was detected in both early and normal cultivation seasons. In addition, genes harbored by qFG3 are related to cell division and differentiation, photosynthesis, and starch synthesis and can also mediate the transition between seed filling and abiotic stress response mechanisms. Rice is susceptible to a variety of diseases throughout its reproductive stage, which is one of the main reasons affecting rice yield. Bacterial blight (BB) is one of the most serious bacterial diseases in rice caused by Xanthomonas oryzaepv.oryzae (Xoo) [4]. Currently, pesticide control is the primary method to control BB. Long-term use of pesticides will result in environmental pollution and the development of pathogen resistance, so the most effective and eco-friendly approach is to breed resistant rice cultivars. Zhu et al. [5] created a single Cas9/gRNA within a 30 bp homologous sequence of the Xa13 and Xa25 genes that targets both, and successfully obtained xa13, xa25, and xa13/xa25 double mutants. The xa13, xa25, and xa13/xa25 double mutants exhibit greater resistance to BB than the wild type (WT) in all five rice varieties. These results provide an effective idea for creating rice cultivars with multiple resistance genes. RD6 is the famous Thailand glutinous rice cultivar, which is popular for its high flavor quality. While it is susceptible to BB and rice blast disease infection. Jirapong et al. [6] pyramided multiple resistance genes by MAS and generated eight near isogenic lines (NILs) of RD6. Nine genotypes, including RD6, were evaluated at three different locations in two consecutive years, and it was found that most of the genotypes (G1, G3, G4, G5, G6, and G7) had higher yield stability than RD6, whereas the stability of yield was poorer in G2 and G8. In case of severe BB disease infection, G2 was able to maintain greater yield while the yield of other genotypes strikingly reduced.

2.2. Research in Maize

Maize is a high-quality food crop with high nutritional value. It is an essential raw material for human food, cultured feed, and industrial production [7]. During the growth of maize, it is susceptible to various kinds of adversity stresses, among which drought is one of the most serious stresses that seriously affects maize yield. The hazard of drought is becoming more severe with climate change and population pressure [8,9]. Yang et al. [10] identified 15 actin depolymerizing factor (ADF) genes in the form of tandem duplication or segmental duplication. Among which, ZmADF5 has been confirmed to be a drought tolerance gene. The analysis of candidate gene association revealed that its promoter region contains three mutation sites associated with drought resistance. In addition, the ADF gene family with a high degree of conservation shows structural similarity. The presence of abundant abiotic stress regulatory elements in the promoter region of the ADF gene family suggests that it has great potential to participate in plant growth and adversity response. With the continuous development of advanced technologies, there is an increasing abundance of methods to analyze the regulatory mechanisms of maize life activities. Maize seed germination, which is directly related to yield and quality, is a complex process involving multiple genes and regulatory networks. Han et al. [11] decoded the molecular mechanism of gibberellin (GA) in the regulation of maize germination by using multi-omics analysis, including transcriptomics, miRNA, and degradome. In the study, differentially expressed genes (DEGs) were identified by RNA-seq, whose number revealed that the regulation of early stages was more complicated since more DEGs were needed than in the later stages. Moreover, miRNA sequencing revealed that the number of differentially expressed miRNAs and their target genes was increased after treatment with GA3, suggesting that GA3 induces more differentially expressed miRNAs to regulate genes associated with maize seed germination and participates in the regulation of maize seed germination. Interestingly, a gene named ZmSLP was found in the glycerophospholipid metabolic pathway, which negatively regulated maize seed germination and inhibited growth at the seedling stage. Maize leaf angle is the angle between the leaf blade and the main stem, and its size is closely related to the photosynthetic efficiency and planting density [12]. He et al. [13] detected a new QTL named qLA2-3 controlling leaf angle, which was finely localized at a physical distance of about 338.46 kb and contained 16 genes in total. Further sequencing and transcriptomics analyses of the NILs identified five candidate genes that may be involved in the regulation of leaf angle.

3. Research in Oilseed Crops

Soybean is one of the widely grown oilseed crops in the world, but its total oil content is much lower than that of peanut. In order to increase the total oil content of soybean, Xu et al. [14] transformed DGAT3, a gene only found in peanut and Arabidopsis, into soybean. It was found that the contents of oleic acid composition and total fatty acid content in transgenic soybean plants overexpressing AhDGAT3 were significantly higher than those of WT. Meanwhile, transgenic soybean plants that overexpressed AhDGAT3 exhibited better agronomic traits compared with WT, including size of pods at different periods, number of effective branches, and weight of seeds at harvest. It was hypothesized that the gene might be related to soybean growth and development. Castor is a special industrial oilseed crop; seed weight and fatty acid content are two main indexes for evaluating its quality. Recently, Peng et al. [15] explored the effect of castor parental combinations on seed weight and fatty acid content of offspring for the first time. It showed that the levels of the indexes in the F1 generation were closely correlated to their parents, with the additive general combining ability and non-additive specific combining ability genetic effects significantly contributing to the changes in fatty acid composition. Moreover, two lines, CSR181 and 20111149, were recommended for use in the castor hybridization program based on the analysis of the comprehensive advantages of combining ability and heritability. Brassica napus L. is a major oilseed crop covered with a layer of wax powder to protect it against external stresses and ensure normal plant growth and development. Zhang et al. [16] found that the formation of wax powder is controlled by two pairs of genes. Through block segregation analysis (BSA) and whole-wide resequencing, the wax gene was localized in a region of 590,663–1,657,546 bp on chromosome A08, where 16 candidate genes were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). It was revealed that three genes showed significant differences in the leaves of waxed and unwaxed parents, and they may inextricably link to wax formation. Brassica oil crops contain a wide range of species and all have indeterminate growth habits, among which Brassica rapa L. is famous for its indeterminate inflorescence [17]. Since indeterminate inflorescences can lead to the appearance of prolonged plant growth and maturity and susceptibility to collapse, which ultimately affects yield, it is crucial to investigate the mode of inheritance and molecular mechanisms that determine inflorescence traits. Chen et al. [18] found that inflorescences are controlled by Brdt1 and Brdt2, and Brdt1 was successfully localized within an interval of approximately 72.7 kb. Furthermore, there is a gene, Bra009508 (BraA10.TFL1), which is homologous to TFL1 in Arabidopsis and may play an important role in controlling the determinant inflorescence trait.

4. Research in Vegetable and Fruits

Flowering Chinese cabbage is prevalent in China due to its exceptional nutritional composition and delightful flavor, whose main edible part is the stem, and yield is directly connected with branching. Gibberellin (GA) is a phytohormone, which is considered an inhibitor of branching that regulates the growth and development of branch buds [19]. Qi et al. [20] investigated the effect of gibberellin on the branching of flowering Chinese cabbage by exogenous spraying of GA3, which showed that GA3 could effectively inhibit the primary rosette branching of it and had a direct impact on the whole plant yield of flowering Chinese cabbage. In addition, auxin-related genes can interact with GA to negatively regulate the number of branches on the rosette stems in flowering Chinese cabbage. Chinese cabbage is another kind of Chinese specialty vegetable that prefers cool and humid environments. Heat stress has an influence on its growth and development and in turn affects its production and quality [21]. The homeodomain leucine zipper (HD-zip) gene family plays an important role in the regulation of carotenoid content, which is closely associated with the color of the inner leaf blades of Chinese cabbage [22,23]. Yin et al. [24] divided the HD-Zip gene family into four subfamilies with three common motifs through research of three Brassicaceae plants. In this study, 14 HD-Zip genes were highly expressed under heat stress treatment in Chinese cabbage, 11 of which were from the HD-Zip I subfamily. Moreover, three genes related to carotenoid content were successfully identified, which also belonged to HD-Zip I. Among them, the expression of the HD-Zip I gene, BraA09g011460.3C, was up-regulated after heat stress treatment but significantly reduced in the carotenoid-rich cultivars, which showed the potential to tolerate heat stress and regulate carotenoid content.

Papaya is a tropical fruit of great commercial and nutritional value. In its growing areas, however, PRSV virus infestation has severely reduced its yield and commercial value. The papaya genome has fewer disease resistance genes, but there are nucleotide-binding site leucine-rich repeat receptor (NLR) family genes in its genome that exert a unique disease resistance role [25,26]. In order to provide a new perspective on disease resistance breeding in papaya, Jiang et al. [27] conducted a comprehensive analysis of the 59 NLR gene in the papaya genome. It was shown that papaya retains all NLR subclasses, and the dominated subclass is coiled-coil(CC)-NBS-LRR(CNL). Meanwhile, they speculate that relatively conserved resistance to powdery mildew8(RPW8)-NBS-LRs(RNLs) and CNLs may help relatively abundant toll/interleukin-1 receptor (TIR)-NBS-LRRs(TNLs) and CNLs to recognize variable pathogen effectors triggering immune responses in papaya. In addition, an insertion cluster of five duplicated CNLs was identified in the papaya genome, where dosage effects and expression divergence of disease resistance genes during evolution were observed. Three genes of this cluster were also strongly correlated to fungal infection. Pineapple is a tropical fruit with great economic value, but its self-incompatibility limits industrialization progress. Selection and breeding of new pineapple cultivars is a vital measure to improve pineapple yield and promote industrialization. Single nucleotide polymorphism (SNP) markers, as a new generation of molecular markers, have verified hybrid authenticity in several crops but have not yet been applied to the study of pineapple F₁ generation. Jia et al. [28] successfully identified the F₁ hybrid generation of pineapple, which was constructed with male parent ‘MD2’ and female parent ‘Josapine’ with a true hybridization rate of 87.58% based on SNP molecular markers. In addition, clustering analysis involving the parents and 313 hybrid offspring revealed that 68.5% of offspring aggregated with ‘MD2’, while only 31.95% were grouped with ‘Josapine’. This study facilitates rapid and accurate identification of target progeny at the seedling stage, which will improve selection efficiency and ensure superior traits in planted cultivars.

5. Research in Other Crops

Leucaena leucocephala (Lam.) de Wit is a mimosoid legume genus plant with high protein content, which has been popularized for livestock feeding in some regions. Currently, hybrid triploids have been successfully created among Leucaena species [29]. Han et al. [30] identified transcriptome-based genetic variation in 21 Leucaena taxa for the first time and established an efficient and high-throughput platform for the rapid identification of triploids in Leucaena. Tartary buckwheat is a flavonoid-rich medicinal plant with anti-inflammatory, antiviral, and anti-allergic properties. However, it often encounters abiotic stresses, including drought and high salt, due to the constraints of the growing environment, which affects its medicinal quality and yield. The mitogen-activated protein kinase (MAPK) signaling cascade is one of the most common signaling pathways in plants, which casts a significant function in the process of abiotic stress. Dong et al. [31] identified 16 MAPK family genes based on the conserved structural domains of MAPK in Tartary buckwheat and analyzed their expression level. The results showed that 15 genes were significantly expressed variably in different organs, indicating that MAPKs are pivotal in Tartary buckwheat growth and development. Furthermore, the expression of FtMAPKs was also analyzed under drought and salt stress, in which 12 and 14 genes, respectively, showed significant expression variations with drought and salt treatment. Meanwhile, three candidate genes, FtMAPK3, FtMAPK4, and FtMAPK8, demonstrated significant expression changes across both abiotic stress treatments.

6. Conclusions and Perspective

In conclusion, we reviewed studies of different crops on yield, quality, resistance, and stress tolerance, which provide new ideas for genetic improvement of crops and the progression of agricultural production. With the emergence of new technologies, genetic improvement means of plant biotechnology will be more abundant; the transformation and application of research results will progress to the realization of sustainable development in agriculture.