Quantitative trait loci analysis of phenotypic traits and principal components of maize tassel inflorescence architecture

Hotspot Regions of Quantitative Trait Loci and Candidate Genes for Ear-Related Traits in Maize: A Literature Review

In this study, hotspot regions, QTL clusters, and candidate genes for eight ear-related traits of maize (ear length, ear diameter, kernel row number, kernel number per row, kernel length, kernel width, kernel thickness, and 100-kernel weight) were summarized and analyzed over the past three decades. This review aims to (1) comprehensively summarize and analyze previous studies on QTLs associated with these eight ear-related traits and identify hotspot bin regions located on maize chromosomes and key candidate genes associated with the ear-related traits and (2) compile major and stable QTLs and QTL clusters from various mapping populations and mapping methods and techniques providing valuable insights for fine mapping, gene cloning, and breeding for high-yield and high-quality maize. Previous research has demonstrated that QTLs for ear-related traits are distributed across all ten chromosomes in maize, and the phenotypic variation explained by a single QTL ranged from 0.40% to 36.76%. In total, 23 QTL hotspot bins for ear-related traits were identified across all ten chromosomes. The most prominent hotspot region is bin 4.08 on chromosome 4 with 15 QTLs related to eight ear-related traits. Additionally, this study identified 48 candidate genes associated with ear-related traits. Out of these, five have been cloned and validated, while twenty-eight candidate genes located in the QTL hotspots were defined by this study. This review offers a deeper understanding of the advancements in QTL mapping and the identification of key candidates associated with eight ear-related traits. These insights will undoubtedly assist maize breeders in formulating strategies to develop higher-yield maize varieties, contributing to global food security.

Deploying QTL-seq rapid identification and separation of the major QTLs of tassel branch number for fine-mapping in advanced maize populations

The tassel competes with the ear for nutrients and shields the upper leaves, thereby reducing the yield of grain. The tassel branch number (TBN) is a pivotal determinant of tassel size, wherein the reduced TBN has the potential to enhance the transmission of light and reduce the consumption of nutrients, which should ultimately result in increased yield. Consequently, the TBN has emerged as a vital target trait in contemporary breeding programs that focus on compact maize varieties. In this study, QTL-seq technology and advanced population mapping were used to rapidly identify and dissect the major effects of the TBN on QTL. Advanced mapping populations (BC4F2 and BC4F3) were derived from the inbred lines 18-599 (8-11 TBN) and 3237 (0-1 TBN) through phenotypic recurrent selection. First, 13 genomic regions associated with the TBN were detected using quantitative trait locus (QTL)-seq and were located on chromosomes 2 and 5. Subsequently, validated loci within these regions were identified by QTL-seq. Three QTLs for TBN were identified in the BC4F2 populations by traditional QTL mapping, with each QTL explaining the phenotypic variation of 6.13-18.17%. In addition, for the major QTL (qTBN2-2 and qTBN5-1), residual heterozygous lines (RHLs) were developed from the BC4F2 population. These two major QTLs were verified in the RHLs by QTL mapping, with the phenotypic variation explained (PVE) of 21.57% and 30.75%, respectively. Near-isogenic lines (NILs) of qTBN2-2 and qTBN5-1 were constructed. There were significant differences between the NILs in TBN. These results will enhance our understanding of the genetic basis of TBN and provide a solid foundation for the fine-mapping of TBN.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01431-y.

Interspecies transfer of RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture

Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize (Zea mays) RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in sorghum (Sorghum bicolor, Sb) and green millet (Setaria viridis, Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate the functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum, and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the nonframeshifted downstream copy, complemented ra1-R branching defects and induced unusual fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of a SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.

Genome wide association analysis for yield related traits in maize

BACKGROUND

Understanding the genetic basis of yield related traits contributes to the improvement of grain yield in maize.

RESULTS

Using 291 excellent maize inbred lines as materials, six yield related traits of maize, including grain yield per plant (GYP), grain length (GL), grain width (GW), kernel number per row (KNR), 100 kernel weight (HKW) and tassel branch number (TBN) were investigated in Jinan, in 2017, 2018 and 2019. The average values of three environments were taken as the phenotypic data of yield related traits, and they were statistically analyzed. Based on 38,683 high-quality SNP markers in the whole genome of the association panel, the MLM with PCA model was used for genome-wide association analysis (GWAS) to obtain 59 significantly associated SNP sites. Moreover, 59 significantly associated SNPs (P < 0.0001) referring to GYP, GL, GW, KNR, HKW and TBN, of which 14 SNPs located in yield related QTLs/QTNs previously reported. A total of 66 candidate genes were identified based on the 59 significantly associated SNPs, of which 58 had functional annotation.

CONCLUSIONS

Using genome-wide association analysis strategy to identify genetic loci related to maize yield, a total of 59 significantly associated SNP were detected. Those results aid in our understanding of the genetic architecture of maize yield and provide useful SNPs for genetic improvement of maize.

Genetic Structure and Molecular Mechanisms Underlying the Formation of Tassel, Anther, and Pollen in the Male Inflorescence of Maize (Zea mays L.)

Maize tassel is the male reproductive organ which is located at the plant's apex; both its morphological structure and fertility have a profound impact on maize grain yield. More than 40 functional genes regulating the complex tassel traits have been cloned up to now. However, the detailed molecular mechanisms underlying the whole process, from male inflorescence meristem initiation to tassel morphogenesis, are seldom discussed. Here, we summarize the male inflorescence developmental genes and construct a molecular regulatory network to further reveal the molecular mechanisms underlying tassel-trait formation in maize. Meanwhile, as one of the most frequently studied quantitative traits, hundreds of quantitative trait loci (QTLs) and thousands of quantitative trait nucleotides (QTNs) related to tassel morphology have been identified so far. To reveal the genetic structure of tassel traits, we constructed a consensus physical map for tassel traits by summarizing the genetic studies conducted over the past 20 years, and identified 97 hotspot intervals (HSIs) that can be repeatedly mapped in different labs, which will be helpful for marker-assisted selection (MAS) in improving maize yield as well as for providing theoretical guidance in the subsequent identification of the functional genes modulating tassel morphology. In addition, maize is one of the most successful crops in utilizing heterosis; mining of the genic male sterility (GMS) genes is crucial in developing biotechnology-based male-sterility (BMS) systems for seed production and hybrid breeding. In maize, more than 30 GMS genes have been isolated and characterized, and at least 15 GMS genes have been promptly validated by CRISPR/Cas9 mutagenesis within the past two years. We thus summarize the maize GMS genes and further update the molecular regulatory networks underlying male fertility in maize. Taken together, the identified HSIs, genes and molecular mechanisms underlying tassel morphological structure and male fertility are useful for guiding the subsequent cloning of functional genes and for molecular design breeding in maize. Finally, the strategies concerning efficient and rapid isolation of genes controlling tassel morphological structure and male fertility and their application in maize molecular breeding are also discussed.

Genetic Diversity of Ancient Camellia sinensis (L.) O.Kuntze in Sandu County of Guizhou Province in China

The ancient tea plant germplasm is an important resource for breeding new tea plant varieties and has great economic value. However, due to man-made and natural disturbances, it has become endangered. In order to have a better management of the conserved tea plant germplasm, it is a requirement to understand the genetic and phenotypic diversity. The aim of this study was to evaluate the genetic and phenotypic diversity of 145 ancient tea plant germplasm resources from five populations in Sandu County of Guizhou province in China. To explore the population genetics of tea plant, we successfully identified 15 simple sequence repeat (SSR) markers, which were highly polymorphic. Additionally, we applied traditional phenotypic methods to evaluate the tea plant diversity. The results suggested that the genetic and phenotypic diversity were relatively high. A total of 96 alleles were identified, and the mean polymorphic information content (PIC) value was found to be 0.66. The analysis of molecular variance (AMOVA) showed that genetic variation within the populations was greater than among the populations. Overall, our results are the valuable baseline data in developing more efficient management and breeding plans for one of the most popular non-alcoholic beverage crops, the tea plant species.

QDtbn1 , an F-box gene affecting maize tassel branch number by a dominant model

Tassel branch number (TBN) is one of the important agronomic traits that directly contribute to grain yield in maize (Zea mays L.), and identification of genes precisely regulating TBN in the parental lines is important for maize hybrid breeding. In this study, a quantitative trait nucleotide (QTN), Q^Dtbn1 , related to tassel branch number was identified using a testcrossing association mapping population through association mapping with the Indels/SNPs in the 5'-UTR (untranslated region) of Zm00001d053358, which encodes a Kelch repeat-containing F-box protein. Q^Dtbn1 was further confirmed to be associated with TBN by a dominant model using an F₂ population, and over-expressing of the candidate gene resulted in a decreasing of TBN, implying that Q^Dtbn1 was governed by the candidate gene with a negative model. This makes Q^Dtbn1 very useful in maize hybrid breeding. Q^Dtbn1 could interact with a maize Skp1-like protein and a SnRK1 protein, and the SnRK1 could also interact with a SnRK2.8 protein. In addition, quantitative real-time PCR assay showed that five substrates of SnRK2 were down-regulated in the over-expressed plants. These imply that the SCF (Skp1/Cul1/F-box protein/Roc1) complex and ABA signal pathway might be involved in the modulation of TBN in maize.

Fine mapping and candidate gene prediction of a major quantitative trait locus for tassel branch number in maize

Tassel branch number (TBN) is the principal component of tassel inflorescence architecture in the maize plant. TBN is believed to be controlled by a set of quantitative trait loci (QTLs). However, it is necessary to identify and genetically evaluate these QTLs before the TBN can be improved upon using a molecular breeding approach. Therefore, in this study, we developed the chromosome segment introgression line (CSIL) TBN1 with the Zong31 (Z31) background and a higher TBN, and then we utilized the CSIL-TBN1-derived populations and identified a major QTL, qTBN6a, by linkage analysis. Fine mapping of the qTBN6a QTL was validated using a set of sub-CSILs and located in a 240-kb genomic region (Bin6.07) in B73RefGen_v4. One allele included in the introgression fragment had a positive effect, noticeably increasing the TBN and demonstrating the potential to improve the TBN of Z31. Afterward, in the qTBN6a interval, gene expression, sequence alignment, functional analysis, and the analysis of motifs in the 5' UTR suggested that candidate genes of qTBN6a are important functional genes at the early stage of immature infected tassel development. Among these candidate genes, a long W22::Mu-insertion/deletion in exon one and an 11-bp insertion/deletion in the promoter region may affect the variation of the qTBN6a QTL observed between Z31 and TBN1. In addition, the candidate genes of qTBN6a were found to encode a pentatricopeptide repeat (PPR)-containing protein and a histone deacetylase (HDA), which are known to be closely associated with RNA editing and stability and chromatin state activity for the transcription of gene expression, respectively. Finally, a model of qTBN6a based on the synergistic regulation of PPR and HDA for the maintenance of inflorescence meristem (IM) identity and its differentiation to the branch meristem (BM) in TBN1 was suggested. Collectively, our results provide an available locus for the molecular improvement of TBN and the isolation of functional genes underlying this QTL.

Combination of multi-locus genome-wide association study and QTL mapping reveals genetic basis of tassel architecture in maize

Maize tassel architecture is a complex quantitative trait that is significantly correlated with biomass yield and grain yield. The present study evaluated the major trait of maize tassel architecture, namely, tassel branch number (TBN), in an association population of 359 inbred lines and an IBM Syn 10 population of 273 doubled haploid lines across three environments. Approximately 43,958 high-quality single nucleotide polymorphisms were utilized to detect significant QTNs associated with TBN based on new multi-locus genome-wide association study methods. There were 30, 38, 73, 40, 47, and 53 QTNs associated with tassel architecture that were detected using the FastmrEMMA, FastmrMLM, EM-BLASSO, mrMLM, pkWMEB, and pLARmEB models, respectively. Among these QTNs, 51 were co-identified by at least two of these methods. In addition, 12 QTNs were consistently detected across multiple environments. Furthermore, 19 QTLs distributed on chromosomes 1, 2, 3, 4, 6, and 7 were detected in 3 environments and the BLUP model based on 6618 bin markers, which explained 3.64-10.96% of the observed phenotypic variations in TBN. Of these, three QTLs were co-detected in two environments. One QTN associated with TBN was localized to one QTL. Approximately 55 candidate genes were detected by common QTNs and LD criteria. One candidate gene, Zm00001d016615, was identified as a putative target of the RA1 gene. Meanwhile, RA1 was previously validated to plays an important role in tassel development. In addition, the newly identified candidate genes Zm00001d003939, Zm00001d030212, Zm00001d011189, and Zm00001d042794 have been reported to involve in a spikelet meristem identity module. The findings of the present study improve our understanding of the genetic basis of tassel architecture in maize.

Genetic architecture of quantitative flower and leaf traits in a pair of sympatric sister species of Primulina

Flowers and leaves each represent suites of functionally interrelated traits that are often involved in species divergence and local adaptation. However, a major unresolved issue is how the individual component traits that make up a complex trait such as a flower evolve in a coordinated fashion to retain a high degree of functionality. We use a quantitative trait loci (QTL) approach to elucidate the genetic architecture of divergence in flower and leaf traits between the sister species Primulina depressa and Primulina danxiaensis, which grow sympatrically but in contrasting microhabitats. We found that flower traits were controlled by multiple QTL of small effect, while leaf physiological and morphological traits tended to be controlled by QTL of larger effect. The observed floral integration, manifested by a high degree overlap in both individual trait QTL and QTL for principal component scores (PCA QTL), may have been critical for evolutionary divergence of floral morphology in relation to their pollinators. This overlap suggests that direct selection on only one or a few of the component traits could have caused substantial divergence in other floral traits due to genetic correlations, while the low QTL overlap between floral and vegetative traits suggests that these trait suites are genetically unlinked and can evolve independently in response to different selective pressures corresponding to their distinct functions.

Genetic and Molecular Mechanisms of Quantitative Trait Loci Controlling Maize Inflorescence Architecture

The establishment of inflorescence architecture is critical for the reproduction of flowering plant species. The maize plant generates two types of inflorescences, the tassel and the ear, and their architectures have a large effect on grain yield and yield-related traits that are genetically controlled by quantitative trait loci (QTLs). Since ear and tassel architecture are deeply affected by the activity of inflorescence meristems, key QTLs and genes regulating meristematic activity have important impacts on inflorescence development and show great potential for optimizing grain yield. Isolation of yield trait-related QTLs is challenging, but these QTLs have direct application in maize breeding. Additionally, characterization and functional dissection of QTLs can provide genetic and molecular knowledge of quantitative variation in inflorescence architecture. In this review, we summarize currently identified QTLs responsible for the establishment of ear and tassel architecture and discuss the potential genetic control of four ear-related and four tassel-related traits. In recent years, several inflorescence architecture-related QTLs have been characterized at the gene level. We review the mechanisms of these characterized QTLs.

Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays)

BACKGROUND

Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested.

RESULTS

Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs).

CONCLUSIONS

We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

Quantitative trait loci for flowering time and inflorescence architecture in rose

The pattern of development of the inflorescence is an important characteristic in ornamental plants, where the economic value is in the flower. The genetic determinism of inflorescence architecture is poorly understood, especially in woody perennial plants with long life cycles. Our objective was to study the genetic determinism of this characteristic in rose. The genetic architectures of 10 traits associated with the developmental timing and architecture of the inflorescence, and with flower production were investigated in a F(1) diploid garden rose population, based on intensive measurements of phenological and morphological traits in a field. There were substantial genetic variations in inflorescence development traits, with broad-sense heritabilities ranging from 0.82 to 0.93. Genotypic correlations were significant for most (87%) pairs of traits, suggesting either pleiotropy or tight linkage among loci. However, non-significant and low correlations between some pairs of traits revealed two independent developmental pathways controlling inflorescence architecture: (1) the production of inflorescence nodes increased the number of branches and the production of flowers; (2) internode elongation connected with frequent branching increased the number of branches and the production of flowers. QTL mapping identified six common QTL regions (cQTL) for inflorescence developmental traits. A QTL for flowering time and many inflorescence traits were mapped to the same cQTL. Several candidate genes that are known to control inflorescence developmental traits and gibberellin signaling in Arabidopsis thaliana were mapped in rose. Rose orthologues of FLOWERING LOCUS T (RoFT), TERMINAL FLOWER 1 (RoKSN), SPINDLY (RoSPINDLY), DELLA (RoDELLA), and SLEEPY (RoSLEEPY) co-localized with cQTL for relevant traits. This is the first report on the genetic basis of complex inflorescence developmental traits in rose.

Towards molecular breeding of reproductive traits in cereal crops

The transition from vegetative to reproductive phase, flowering per se, floral organ development, panicle structure and morphology, meiosis, pollination and fertilization, cytoplasmic male sterility (CMS) and fertility restoration, and grain development are the main reproductive traits. Unlocking their genetic insights will enable plant breeders to manipulate these traits in cereal germplasm enhancement. Multiple genes or quantitative trait loci (QTLs) affecting flowering (phase transition, photoperiod and vernalization, flowering per se), panicle morphology and grain development have been cloned, and gene expression research has provided new information about the nature of complex genetic networks involved in the expression of these traits. Molecular biology is also facilitating the identification of diverse CMS sources in hybrid breeding. Few Rf (fertility restorer) genes have been cloned in maize, rice and sorghum. DNA markers are now used to assess the genetic purity of hybrids and their parental lines, and to pyramid Rf or tms (thermosensitive male sterility) genes in rice. Transgene(s) can be used to create de novo CMS trait in cereals. The understanding of reproductive biology facilitated by functional genomics will allow a better manipulation of genes by crop breeders and their potential use across species through genetic transformation.