Identification of quantitative trait loci for related traits of stalk lodging resistance using genome-wide association studies in maize (Zea mays L.)

Variation and interrelationships in the growth, yield, and lodging of oat under different planting densities

Background

Oat is a dual-purpose cereal used for grain and forage. The demand of oat has been increasing as the understanding of the nutritional, ecological, and economic values of oat increased. However, the frequent lodging during the growing period severely affect the high yielding potential and the quality of the grain and forage of oat.

Methods

Therefore, we used the lodging-resistant variety LENA and the lodging-sensitive variety QY2 as materials, implementing four different planting densities: 2.25×106 plants/ha (D1), 4.5×106 plants/ha (D2), 6.75×106 plants/ha (D3), and 9×106 plants/ha (D4). At the appropriate growth and development stages, we assessed agronomic traits, mechanical characteristics, biochemical compositions, yield and its components. The study investigated the impact of planting density on the growth, lodging, and yield of oat, as well as their interrelationships. Additionally, we identified the optimal planting density to establish a robust crop structure. The research aims to contribute to the high-yield and high-quality cultivation of oat.

Results

We observed that with increasing planting density, plant height, grass and grain yields of both varieties first increased and then decreased; root fresh weight, stem diameter, stem wall thickness, stem puncture strength, breaking strength, compressive strength, lignin and crude fiber contents, and yield components decreased; whereas the lodging rate and lodging coefficient increased. Planting density affects lodging by regulating plant height, height of center of gravity, stem wall thickness, internode length, and root fresh weight of oat. Additionally, it can impact stem mechanical strength by modulating the synthesis of lignin and crude fiber, which in turn affecting lodging resistance. Plant height, height of center of gravity, stem wall thickness, internode length, root fresh weight, breaking strength, compressive strength, lignin and crude fiber content, single-plant weight, grain yield and 1,000-grain weight can serve as important indicators for evaluating oat stem lodging resistance. We also noted that planting density affected grain yield both directly and indirectly (by affecting lodging); high density increased lodging rate and decreased grain yield, mainly by reducing 1,000-grain weight. Nonetheless, there was no significant relationship between lodging and grass yield. As appropriate planting density can increase the yield while maintaining good lodging resistance, in this study, 4.5×106 plants/ha (D2) was found to be the best planting density for oat in terms of lodging resistance and grass and grain yield. These findings can be used as a reference for oat planting.

Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize

Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype-phenotype association across various species. Maize (Zea mays L.), renowned for its extensive genetic diversity and rapid linkage disequilibrium (LD), stands as an exemplary candidate for GWAS. In maize, GWAS has made significant advancements by pinpointing numerous genetic loci and potential genes associated with complex traits, including responses to both abiotic and biotic stress. These discoveries hold the promise of enhancing adaptability and yield through effective breeding strategies. Nevertheless, the impact of environmental stress on crop growth and yield is evident in various agronomic traits. Therefore, understanding the complex genetic basis of these traits becomes paramount. This review delves into current and future prospectives aimed at yield, quality, and environmental stress resilience in maize and also addresses the challenges encountered during genomic selection and molecular breeding, all facilitated by the utilization of GWAS. Furthermore, the integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics has enriched our understanding of intricate traits in maize, thereby enhancing environmental stress tolerance and boosting maize production. Collectively, these insights not only advance our understanding of the genetic mechanism regulating complex traits but also propel the utilization of marker-assisted selection in maize molecular breeding programs, where GWAS plays a pivotal role. Therefore, GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.

Genome-wide association study for stalk lodging resistance related traits in maize (Zea mays L.)

BACKGROUND

The stalk traits stalk diameter, stalk length, rind penetrometer resistance and dry matter content are important indicators for measuring lodging resistance.

RESULTS

In this study, 377 inbred lines were used as the basic materials, and four stalk-related traits including stalk diameter, stalk length, rind penetrometer resistance and dry matter content of the third segment of maize, were investigated at the tasseling, grain filling, and maturity stages. 461,053 high-quality SNPs which were obtained by whole genome resequencing were used for genome-wide association study. As a result of mixed linear model analysis (P < 9.77 × 10-6), 29 significant SNPs related to traits were detected, accounting for 7.19% -15.03% of phenotypic variation, among which 4, 1, 4 and 20 SNPs were found related to rind penetrometer resistance, stalk diameter, stalk length, and dry matter content respectively. Most candidate genes are related to plant element structure, signal transduction mechanisms, inorganic ion transport and metabolism, nucleotide transport and metabolism, and transporter enzyme families. Comparing mixed linear model with generalized linear model, a total of 12 candidate genes were detected repeatedly, during which the candidate gene Zm00001d014449 were detected 5 times, with a phenotypic variation interpretation rate of 9.95% -10.84%. This gene is mainly expressed in cells with active cell division and tissue differentiation, and is involved in the formation of stalk vascular bundles and the synthesis of cell walls. Another candidate gene, Zm00001d005300, encodes the transcription factor MYB44, which regulates the dependence of salt stress signal phosphorylation, can effectively inhibit the accumulation of destructive reactive oxygen species, and has a certain resistance to non-biotic stress. In addition, this study also found that 10 unknown functional genes can be further Functional verification.

CONCLUSIONS

This study helps to deepen the understanding of the genetic basis of traits related to maize stalk lodging resistance, and provides theoretical guidance for future maize lodging resistance breeding.

Phenotypic and genome-wide association analyses for nitrogen use efficiency related traits in maize (Zea mays L.) exotic introgression lines

Nitrogen (N) limits crop production, yet more than half of N fertilizer inputs are lost to the environment. Developing maize hybrids with improved N use efficiency can help minimize N losses and in turn reduce adverse ecological, economical, and health consequences. This study aimed to identify single nucleotide polymorphisms (SNPs) associated with agronomic traits (plant height, grain yield, and anthesis to silking interval) under high and low N conditions. A genome-wide association study (GWAS) was conducted using 181 doubled haploid (DH) lines derived from crosses between landraces from the Germplasm Enhancement of Maize (BGEM lines) project and two inbreds, PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers. The same lines from the per se trials were used as parental lines for the testcross field trials. Plant height, anthesis to silking interval, and grain yield were collected from high and low N conditions in three environments for both per se and testcross trials. We used three GWAS models, namely, general linear model (GLM), mixed linear model (MLM), and Fixed and Random model Circulating Probability Unification (FarmCPU) model. We observed significant genetic variation among the DH lines and their derived testcrosses. Interestingly, some testcrosses of exotic introgression lines were superior under high and low N conditions compared to the check hybrid, PHB47/PHZ51. We detected multiple SNPs associated with agronomic traits under high and low N, some of which co-localized with gene models associated with stress response and N metabolism. The BGEM panel is, thus, a promising source of allelic diversity for genes controlling agronomic traits under different N conditions.