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22 pages, 16409 KiB

Open AccessArticle

Phenotypic Investigation and RNA-seq of KN1 Involved in Leaf Angle Formation in Maize (Zea mays L.)

by Yuanming Wu, Yunfang Zhang, Zelong Zhuang, Xiangzhuo Ji, Jianwen Bian, Jinhong Xian, Yinxia Wang and Yunling Peng

Int. J. Mol. Sci. 2024, 25(6), 3180; https://doi.org/10.3390/ijms25063180 - 10 Mar 2024

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Abstract

Leaf angle (LA) is one of the core agronomic traits of maize, which controls maize yield by affecting planting density. Previous studies have shown that the KN1 gene is closely related to the formation of maize LA, but its specific mechanism has not [...] Read more.

Leaf angle (LA) is one of the core agronomic traits of maize, which controls maize yield by affecting planting density. Previous studies have shown that the KN1 gene is closely related to the formation of maize LA, but its specific mechanism has not been fully studied. In this study, phenotype investigation and transcriptomic sequencing were combined to explore the mechanism of LA changes in wild type maize B73 and mutant kn1 under exogenous auxin (IAA) and abscisic acid (ABA) treatment. The results showed that the effect of exogenous phytohormones had a greater impact on the LA of kn1 compared to B73. Transcriptome sequencing showed that genes involved in IAA, gibberellins (GAs) and brassinosteroids (BRs) showed different differential expression patterns in kn1 and B73. This study provides new insights into the mechanism of KN1 involved in the formation of maize LA, and provides a theoretical basis for breeding maize varieties with suitable LA. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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20 pages, 7749 KiB

Open AccessArticle

Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population

by Yuan Dong, Guoliang Li, Xinghua Zhang, Zhiqian Feng, Ting Li, Zhoushuai Li, Shizhong Xu, Shutu Xu, Wenxin Liu and Jiquan Xue

Int. J. Mol. Sci. 2024, 25(2), 1190; https://doi.org/10.3390/ijms25021190 - 18 Jan 2024

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Abstract

Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 [...] Read more.

Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F₁ hybrid populations, it also provides a valuable basis for further molecular biology and breeding research. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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21 pages, 6425 KiB

Open AccessArticle

Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant Height

by Jie Zhang, Yuxin Xie, Hongwei Zhang, Cheng He, Xiaoli Wang, Yu Cui, Yanfang Heng, Yingchao Lin, Riliang Gu, Jianhua Wang and Junjie Fu

Int. J. Mol. Sci. 2023, 24(11), 9150; https://doi.org/10.3390/ijms24119150 - 23 May 2023

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Abstract

Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics [...] Read more.

Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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23 pages, 3543 KiB

Open AccessArticle

ZmDRR206 Regulates Nutrient Accumulation in Endosperm through Its Role in Cell Wall Biogenesis during Maize Kernel Development

by Yanmei Li, Dongdong Li, Lizhu E, Jiayi Yang, Wenjing Liu, Mingliang Xu and Jianrong Ye

Int. J. Mol. Sci. 2023, 24(10), 8735; https://doi.org/10.3390/ijms24108735 - 13 May 2023

Cited by 2 | Viewed by 1413

Abstract

Dirigent proteins (DIRs) contribute to plant fitness by dynamically reorganizing the cell wall and/or by generating defense compounds during plant growth, development, and interactions with environmental stresses. ZmDRR206 is a maize DIR, it plays a role in maintaining cell wall integrity during seedling [...] Read more.

Dirigent proteins (DIRs) contribute to plant fitness by dynamically reorganizing the cell wall and/or by generating defense compounds during plant growth, development, and interactions with environmental stresses. ZmDRR206 is a maize DIR, it plays a role in maintaining cell wall integrity during seedling growth and defense response in maize, but its role in regulating maize kernel development is unclear. Association analysis of candidate genes indicated that the natural variations of ZmDRR206 were significantly associated with maize hundred-kernel weight (HKW). ZmDRR206 plays a dominant role in storage nutrient accumulation in endosperm during maize kernel development, ZmDRR206 overexpression resulted in small and shrunken maize kernel with significantly reduced starch content and significantly decreased HKW. Cytological characterization of the developing maize kernels revealed that ZmDRR206 overexpression induced dysfunctional basal endosperm transfer layer (BETL) cells, which were shorter with less wall ingrowth, and defense response was constitutively activated in developing maize kernel at 15 and 18 DAP by ZmDRR206 overexpression. The BETL-development-related genes and auxin signal-related genes were down-regulated, while cell wall biogenesis-related genes were up-regulated in developing BETL of the ZmDRR206-overexpressing kernel. Moreover, the developing ZmDRR206-overexpressing kernel had significantly reduced contents of the cell wall components such as cellulose and acid soluble lignin. These results suggest that ZmDRR206 may play a regulatory role in coordinating cell development, storage nutrient metabolism, and stress responses during maize kernel development through its role in cell wall biogenesis and defense response, and provides new insights into understanding the mechanisms of kernel development in maize. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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17 pages, 3618 KiB

Open AccessArticle

Multi-Trait Genomic Prediction Improves Accuracy of Selection among Doubled Haploid Lines in Maize

by Haixiao Hu, Yujie Meng, Wenxin Liu, Shaojiang Chen and Daniel E. Runcie

Int. J. Mol. Sci. 2022, 23(23), 14558; https://doi.org/10.3390/ijms232314558 - 22 Nov 2022

Cited by 1 | Viewed by 1338

Abstract

Recent advances in maize doubled haploid (DH) technology have enabled the development of large numbers of DH lines quickly and efficiently. However, testing all possible hybrid crosses among DH lines is a challenge. Phenotyping haploid progenitors created during the DH process could accelerate [...] Read more.

Recent advances in maize doubled haploid (DH) technology have enabled the development of large numbers of DH lines quickly and efficiently. However, testing all possible hybrid crosses among DH lines is a challenge. Phenotyping haploid progenitors created during the DH process could accelerate the selection of DH lines. Based on phenotypic and genotypic data of a DH population and its corresponding haploids, we compared phenotypes and estimated genetic correlations between the two populations, compared genomic prediction accuracy of multi-trait models against conventional univariate models within the DH population, and evaluated whether incorporating phenotypic data from haploid lines into a multi-trait model could better predict performance of DH lines. We found significant phenotypic differences between DH and haploid lines for nearly all traits; however, their genetic correlations between populations were moderate to strong. Furthermore, a multi-trait model taking into account genetic correlations between traits in the single-environment trial or genetic covariances in multi-environment trials can significantly increase genomic prediction accuracy. However, integrating information of haploid lines did not further improve our prediction. Our findings highlight the superiority of multi-trait models in predicting performance of DH lines in maize breeding, but do not support the routine phenotyping and selection on haploid progenitors of DH lines. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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14 pages, 2308 KiB

Open AccessArticle

Genetic Analysis and Fine Mapping of ZmGHT1 Conferring Glufosinate Herbicide Tolerance in Maize (Zea mays L.)

by Jianxi Bao, Yuexin Gao, Yanan Li, Suowei Wu, Jinping Li, Zhenying Dong and Xiangyuan Wan

Int. J. Mol. Sci. 2022, 23(19), 11481; https://doi.org/10.3390/ijms231911481 - 29 Sep 2022

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Abstract

Weed interference in the crop field is one of the major biotic stresses causing dramatic crop yield losses, and the development of herbicide-resistant crops is critical for weed control in the application of herbicide technologies. To identify herbicide-resistant germplasms, we screened 854 maize [...] Read more.

Weed interference in the crop field is one of the major biotic stresses causing dramatic crop yield losses, and the development of herbicide-resistant crops is critical for weed control in the application of herbicide technologies. To identify herbicide-resistant germplasms, we screened 854 maize inbreed lines and 25,620 seedlings by spraying them with 1 g/L glufosinate. One plant (L336R), possibly derived from a natural variation of line L336, was identified to have the potential for glufosinate tolerance. Genetic analysis validated that the glufosinate tolerance of L336R is conferred by a single locus, which was tentatively designated as ZmGHT1. By constructing a bi-parental population derived from L336R, and a glufosinate sensitive line L312, ZmGHT1 was mapped between molecular markers M9 and M10. Interestingly, genomic comparation between the two sequenced reference genomes showed that large scale structural variations (SVs) occurred within the mapped region, resulting in 2.16 Mb in the inbreed line B73, and 11.5 kb in CML277, respectively. During the fine mapping process, we did not detect any additional recombinant, even by using more than 9500 F₂ and F₃ plants, suspecting that SVs should also have occurred between L336R and L312 in this region, which inhibited recombination. By evaluating the expression of the genes within the mapped interval and using functional annotation, we predict that the gene Zm00001eb361930, encoding an aminotransferase, is the most likely causative gene. After glufosinate treatment, lower levels of ammonia content and a higher activity of glutamine synthetase (GS) in L336R were detected compared with those of L336 and L312, suggesting that the target gene may participate in ammonia elimination involving GS activity. Collectively, our study can provide a material resource for maize herbicide resistant breeding, with the potential to reveal a new mechanism for herbicide resistance. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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17 pages, 2567 KiB

Open AccessArticle

Combined QTL Mapping across Multiple Environments and Co-Expression Network Analysis Identified Key Genes for Embryogenic Callus Induction from Immature Maize Embryos

by Yun Long, Tianhu Liang, Langlang Ma, Peng Liu, Yun Yang, Xiaoling Zhang, Chaoying Zou, Minyan Zhang, Fei Ge, Guangsheng Yuan, Thomas Lübberstedt, Guangtang Pan and Yaou Shen

Int. J. Mol. Sci. 2022, 23(15), 8786; https://doi.org/10.3390/ijms23158786 - 07 Aug 2022

Cited by 2 | Viewed by 1852

Abstract

The ability of immature embryos to induce embryogenic callus (EC) is crucial for genetic transformation in maize, which is highly genotype-dependent. To dissect the genetic basis of maize EC induction, we conducted QTL mapping for four EC induction-related traits, the rate of embryogenic [...] Read more.

The ability of immature embryos to induce embryogenic callus (EC) is crucial for genetic transformation in maize, which is highly genotype-dependent. To dissect the genetic basis of maize EC induction, we conducted QTL mapping for four EC induction-related traits, the rate of embryogenic callus induction (REC), rate of shoot formation (RSF), length of shoot (LS), and diameter of callus (DC) under three environments by using an IBM Syn10 DH population derived from a cross of B73 and Mo17. These EC induction traits showed high broad-sense heritability (>80%), and significantly negative correlations were observed between REC and each of the other traits across multiple environments. A total of 41 QTLs for EC induction were identified, among which 13, 12, 10, and 6 QTLs were responsible for DC, RSF, LS, and REC, respectively. Among them, three major QTLs accounted for >10% of the phenotypic variation, including qLS1-1 (11.54%), qLS1-3 (10.68%), and qREC4-1 (11.45%). Based on the expression data of the 215 candidate genes located in these QTL intervals, we performed a weighted gene co-expression network analysis (WGCNA). A combined use of KEGG pathway enrichment and eigengene-based connectivity (KME) values identified the EC induction-associated module and four hub genes (Zm00001d028477, Zm00001d047896, Zm00001d034388, and Zm00001d022542). Gene-based association analyses validated that the variations in Zm00001d028477 and Zm00001d034388, which were involved in tryptophan biosynthesis and metabolism, respectively, significantly affected EC induction ability among different inbred lines. Our study brings novel insights into the genetic and molecular mechanisms of EC induction and helps to promote marker-assisted selection of high-REC varieties in maize. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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Review

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21 pages, 3317 KiB

Open AccessReview

ATP-Binding Cassette G Transporters and Their Multiple Roles Especially for Male Fertility in Arabidopsis, Rice and Maize

by Suowei Wu, Chaowei Fang, Ziwen Li, Yanbo Wang, Shuangshuang Pan, Yuru Wu, Xueli An, Yan Long and Xiangyuan Wan

Int. J. Mol. Sci. 2022, 23(16), 9304; https://doi.org/10.3390/ijms23169304 - 18 Aug 2022

Cited by 7 | Viewed by 2073

Abstract

ATP-binding cassette subfamily G (ABCG) transporters are extensive in plants and play essential roles in various processes influencing plant fitness, but the research progress varies greatly among Arabidopsis, rice and maize. In this review, we present a consolidated nomenclature and characterization of [...] Read more.

ATP-binding cassette subfamily G (ABCG) transporters are extensive in plants and play essential roles in various processes influencing plant fitness, but the research progress varies greatly among Arabidopsis, rice and maize. In this review, we present a consolidated nomenclature and characterization of the whole 51 ABCG transporters in maize, perform a phylogenetic analysis and classification of the ABCG subfamily members in maize, and summarize the latest research advances in ABCG transporters for these three plant species. ABCG transporters are involved in diverse processes in Arabidopsis and rice, such as anther and pollen development, vegetative and female organ development, abiotic and biotic stress response, and phytohormone transport, which provide useful clues for the functional investigation of ABCG transporters in maize. Finally, we discuss the current challenges and future perspectives for the identification and mechanism analysis of substrates for plant ABCG transporters. This review provides a basic framework for functional research and the potential application of ABCG transporters in multiple plants, including maize. Full article

(This article belongs to the Special Issue Advances and Innovations in Maize Genetics and Breeding Research)

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