Nucleotide diversity of Maize ZmBT1 gene and association with starch physicochemical properties

Nucleotide polymorphisms of the maize ZmFWL7 gene and their association with ear-related traits

Plant fw2.2-like (FWL) genes, encoding proteins harboring a placenta-specific eight domain, have been suggested to control fruit and grain size through regulating cell division, differentiation, and expansion. Here, we re-sequenced the nucleotide sequences of the maize ZmFWL7 gene, a member of the FWL family, in 256 elite maize inbred lines, and the associations of nucleotide polymorphisms in this locus with 11 ear-related traits were further detected. A total of 175 variants, including 159 SNPs and 16 InDels, were identified in the ZmFWL7 locus. Although the promoter and downstream regions showed higher nucleotide polymorphism, the coding region also possessed 61 SNPs and 6 InDels. Eleven polymorphic sites in the ZmFWL7 locus were found to be significantly associated with eight ear-related traits. Among them, two nonsynonymous SNPs (SNP2370 and SNP2898) showed significant association with hundred kernel weight (HKW), and contributed to 7.11% and 8.62% of the phenotypic variations, respectively. In addition, the SNP2898 was associated with kernel width (KW), and contributed to 7.57% of the phenotypic variations. Notably, the elite allele T of SNP2370 was absent in teosintes and landraces, while its frequency in inbred lines was increased to 12.89%. By contrast, the frequency of the elite allele A of SNP2898 was 3.12% in teosintes, and it was raised to 12.68% and 19.92% in landraces and inbred lines, respectively. Neutral tests show that this locus wasn’t artificially chosen during the process of domestication and genetic improvement. Our results revealed that the elite allelic variants in ZmFWL7 might possess potential for the genetic improvement of maize ear-related traits.

Nucleotide Diversity of the Maize ZmCNR13 Gene and Association With Ear Traits

The maize (Zea mays L.) ZmCNR13 gene, encoding a protein of fw2.2-like (FWL) family, has been demonstrated to be involved in cell division, expansion, and differentiation. In the present study, the genomic sequences of the ZmCNR13 locus were re-sequenced in 224 inbred lines, 56 landraces and 30 teosintes, and the nucleotide polymorphism and selection signature were estimated. A total of 501 variants, including 415 SNPs and 86 Indels, were detected. Among them, 51 SNPs and 4 Indels were located in the coding regions. Although neutrality tests revealed that this locus had escaped from artificial selection during the process of maize domestication, the population of inbred lines possesses lower nucleotide diversity and decay of linkage disequilibrium. To estimate the association between sequence variants of ZmCNR13 and maize ear characteristics, a total of ten ear-related traits were obtained from the selected inbred lines. Four variants were found to be significantly associated with six ear-related traits. Among them, SNP2305, a non-synonymous mutation in exon 2, was found to be associated with ear weight, ear grain weight, ear diameter and ear row number, and explained 4.59, 4.61, 4.31, and 8.42% of the phenotypic variations, respectively. These results revealed that natural variations of ZmCNR13 might be involved in ear development and can be used in genetic improvement of maize ear-related traits.

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.

Genome-wide association study for kernel composition and flour pasting behavior in wholemeal maize flour

BACKGROUND

Maize is a crop in high demand for food purposes and consumers worldwide are increasingly concerned with food quality. However, breeding for improved quality is a complex task and therefore developing tools to select for better quality products is of great importance. Kernel composition, flour pasting behavior, and flour particle size have been previously identified as crucial for maize-based food quality. In this work we carried out a genome-wide association study to identify genomic regions controlling compositional and pasting properties of maize wholemeal flour.

RESULTS

A collection of 132 diverse inbred lines, with a considerable representation of the food used Portuguese unique germplasm, was trialed during two seasons, and harvested samples characterized for main compositional traits, flour pasting parameters and mean particle size. The collection was genotyped with the MaizeSNP50 array. SNP-trait associations were tested using a mixed linear model accounting for genetic relatedness. Fifty-seven genomic regions were identified, associated with the 11 different quality-related traits evaluated. Regions controlling multiple traits were detected and potential candidate genes identified. As an example, for two viscosity parameters that reflect the capacity of the starch to absorb water and swell, the strongest common associated region was located near the dull endosperm 1 gene that encodes a starch synthase and is determinant on the starch endosperm structure in maize.

CONCLUSIONS

This study allowed for identifying relevant regions on the maize genome affecting maize kernel composition and flour pasting behavior, candidate genes for the majority of the quality-associated genomic regions, or the most promising target regions to develop molecular tools to increase efficacy and efficiency of quality traits selection (such as "breadability") within maize breeding programs.

TaBT1, affecting starch synthesis and thousand kernel weight, underwent strong selection during wheat improvement

BRITTLE1 (BT1), responsible for unidirectional transmembrane transport of ADP-glucose, plays a pivotal role in starch synthesis of cereal grain. In this study, we isolated three TaBT1 homoeologous genes located on chromosomes 6A, 6B, and 6D in common wheat. TaBT1 was mainly expressed in developing grains, and knockdown of TaBT1 in common wheat produced a decrease in grain size, thousand kernel weight (TKW), and grain total starch content. High diversity was detected at the TaBT1-6B locus, with 24 polymorphic sites forming three haplotypes (Hap1, Hap2, and Hap3). Association analysis revealed that Hap1 and Hap2 were preferred haplotypes in modern breeding, for their significant correlations with higher TKW. Furthermore, β-glucuronidase (GUS) staining and enzyme activity assays in developing grains of transgenic rice with exogenous promoters indicated that the promoters of Hap1 and Hap2 showed stronger driving activity than that of Hap3. Evolutionary analysis revealed that BT1 underwent strong selection during wheat polyploidization. In addition, the frequency distribution of TaBT1-6B haplotypes revealed that Hap1 and Hap2 were preferred in global modern wheat cultivars. Our findings suggest that TaBT1 has an important effect on starch synthesis and TKW, and provide two valuable molecular markers for marker assisted selection (MAS) in wheat high-yield breeding.

Genome-Wide Association Mapping of Starch Pasting Properties in Maize Using Single-Locus and Multi-Locus Models

Maize starch plays a critical role in food processing and industrial application. The pasting properties, the most important starch characteristics, have enormous influence on fabrication property, flavor characteristics, storage, cooking, and baking. Understanding the genetic basis of starch pasting properties will be beneficial for manipulation of starch properties for a given purpose. Genome-wide association studies (GWAS) are becoming a powerful tool for dissecting the complex traits. Here, we carried out GWAS for seven pasting properties of maize starch with a panel of 230 inbred lines and 145,232 SNPs using one single-locus method, genome-wide efficient mixed model association (GEMMA), and three multi-locus methods, FASTmrEMMA, FarmCPU, and LASSO. We totally identified 60 quantitative trait nucleotides (QTNs) for starch pasting properties with these four GWAS methods. FASTmrEMMA detected the most QTNs (29), followed by FarmCPU (19) and LASSO (12), GEMMA detected the least QTNs (7). Of these QTNs, seven QTNs were identified by more than one method simultaneously. We further investigated locations of these significantly associated QTNs for possible candidate genes. These candidate genes and significant QTNs provide the guidance for further understanding of molecular mechanisms of starch pasting properties. We also compared the statistical powers and Type I errors of the four GWAS methods using Monte Carlo simulations. The results suggest that the multi-locus method is more powerful than the single-locus method and a combination of these multi-locus methods could help improve the detection power of GWAS.