Genetic basis of maize stalk strength decoded via linkage and association mapping.

Stalk lodging is a severe problem that limits maize production worldwide, although little attention has been given to its genetic basis. Here we measured rind penetrometer resistance (RPR), an effective index for stalk lodging, in a multi-parent population of 1948 recombinant inbred lines (RILs) and an association population of 508 inbred lines (AMP508). Linkage and association mapping identified 53 and 29 single quantitative trait loci (QTLs) and 50 and 19 pairs of epistatic interactions for RPR in the multi-parent population and AMP508 population, respectively. Phenotypic variation explained by all identified epistatic QTLs (up to ~5%) was much less than that explained by all single additive QTLs (up to ~33% in the multi-parent population and ~ 60% in the AMP508 population). Among all detected QTLs, only eight single QTLs explained >10% of phenotypic variation in single RIL populations. Alleles that increased RPR were enriched in tropical/subtropical (TST) groups from the AMP508 population. Based on genome-wide association studies in both populations, we identified 137 candidate genes affecting RPR, which were assigned to multiple biological processes, such as the biosynthesis of cell wall components. Sixty-six candidate genes were cross-validated by multiple methods or populations. Most importantly, 23 candidate genes were upregulated or downregulated in high-RPR lines relative to low-RPR lines, supporting the associations between candidate genes and RPR. These findings reveal the complex nature of the genetic basis underlying RPR and provide loci or candidate genes for developing elite varieties that are resistant to stalk lodging via molecular breeding.

A high-throughput phenotyping method for sugarcane rind penetrometer resistance and breaking force characterization by near-infrared spectroscopy.

BACKGROUND: Sugarcane (Saccharum spp.) is the core crop for sugar and bioethanol production over the world. A major problem in sugarcane production is stalk lodging due to weak mechanical strength. Rind penetrometer resistance (RPR) and breaking force are two kinds of regular parameters for mechanical strength characterization. However, due to the lack of efficient methods for determining RPR and breaking force in sugarcane, genetic approaches for improving these traits are generally limited. This study was designed to use near-infrared spectroscopy (NIRS) calibration assay to accurately assess mechanical strength on a high-throughput basis for the first time. RESULTS: Based on well-established laboratory measurements of sugarcane stalk internodes collected in the years 2019 and 2020, considerable variations in RPR and breaking force were observed in the stalk internodes. Following a standard NIRS calibration process, two online models were obtained with a high coefficient of determination (R2) and the ratio of prediction to deviation (RPD) values during calibration, internal cross-validation, and external validation. Remarkably, the equation for RPR exhibited R2 and RPD values as high as 0.997 and 17.70, as well as showing relatively low root mean square error values at 0.44 N mm-2 during global modeling, demonstrating excellent predictive performance. CONCLUSIONS: This study delivered a successful attempt for rapid and precise prediction of rind penetrometer resistance and breaking force in sugarcane stalk by NIRS assay. These established models can be used to improve phenotyping jobs for sugarcane germplasm on a large scale.

Integrating biochemical and anatomical characterizations with transcriptome analysis to dissect superior stem strength of ZS11 (Brassica napus).

Stem lodging resistance is a serious problem impairing crop yield and quality. ZS11 is an adaptable and stable yielding rapeseed variety with excellent resistance to lodging. However, the mechanism regulating lodging resistance in ZS11 remains unclear. Here, we observed that high stem mechanical strength is the main factor determining the superior lodging resistance of ZS11 through a comparative biology study. Compared with 4D122, ZS11 has higher rind penetrometer resistance (RPR) and stem breaking strength (SBS) at flowering and silique stages. Anatomical analysis shows that ZS11 exhibits thicker xylem layers and denser interfascicular fibrocytes. Analysis of cell wall components suggests that ZS11 possessed more lignin and cellulose during stem secondary development. By comparative transcriptome analysis, we reveal a relatively higher expression of genes required for S-adenosylmethionine (SAM) synthesis, and several key genes (4-COUMATATE-CoA LIGASE, CINNAMOYL-CoA REDUCTASE, CAFFEATE O-METHYLTRANSFERASE, PEROXIDASE) involved in lignin synthesis pathway in ZS11, which support an enhanced lignin biosynthesis ability in the ZS11 stem. Moreover, the difference in cellulose may relate to the significant enrichment of DEGs associated with microtubule-related process and cytoskeleton organization at the flowering stage. Protein interaction network analysis indicate that the preferential expression of several genes, such as LONESOME HIGHWAY (LHW), DNA BINDING WITH ONE FINGERS (DOFs), WUSCHEL HOMEOBOX RELATED 4 (WOX4), are related to vascular development and contribute to denser and thicker lignified cell layers in ZS11. Taken together, our results provide insights into the physiological and molecular regulatory basis for the formation of stem lodging resistance in ZS11, which will greatly promote the application of this superior trait in rapeseed breeding.

Genetic Architecture of Maize Stalk Diameter and Rind Penetrometer Resistance in a Recombinant Inbred Line Population.

Stalk lodging presents a major constraint on maize (Zea mays L.) quantity and quality and hampers mechanized grain harvesting. Stalk diameter (SD) and rind penetrometer resistance (RPR) are crucial indicators of stalk lodging. To dissect the genetic architecture of these indicators, we constructed a recombinant inbred line (RIL) population derived from a cross between maize inbred lines LDC-1 and YS501 to identify quantitative trait loci (QTLs) controlling SD and RPR. Corresponding phenotypes of basal second, third, and fourth internodes in four environments were determined. By integrating QTL mapping results based on individual environments and best linear unbiased prediction (BLUP) values, we identified 12, 12, and 13 QTLs associated with SD and 17, 14, and 17 associated with RPR. Each QTL accounted for 3.83-21.72% of phenotypic variation. For SD-related QTLs, 30 of 37 were enriched in 12 QTL clusters; similarly, RPR-related QTLs had 38 of 48 enriched in 12 QTL clusters. The stable QTL qSD9-2 for SD on chromosome 9 was validated and delimited within a physical region of 9.97 Mb. Confidence intervals of RPR-related QTLs contained 169 genes involved in lignin and polysaccharide biosynthesis, with 12 of these less than 500 kb from the peak of the corresponding QTL. Our results deepen our understanding of the genetic mechanism of maize stalk strength and provide a basis for breeding lodging resistance.

Physical properties of a sandy soil as affected by incubation with a synthetic root exudate: Strength, thermal and hydraulic conductivity, and evaporation.

Plant roots release various organic materials that may modify soil structure and affect heat and mass transfer processes. The objective of this study was to determine the effects of a synthetic root exudate (SRE) on penetrometer resistance (PR), thermal conductivity (λ), hydraulic conductivity (k) and evaporation of water in a sandy soil. Soil samples, mixed with either distilled water or the SRE, were packed into columns at a designated bulk density and water content, and incubated for 7 days at 18°C. Soil PR, λ, k and evaporation rate were monitored during drying processes. Compared with those incubated with water, samples incubated with SRE had visible hyphae, greater PR (0.7-5.5 MPa in the water content range of 0.11 to 0.22 m3 m-3) and λ (0.2-0.7 W m-1 K-1 from 0.05 to 0.22 m3 m-3), and increased k in the wet region but decreased k in the dry region. SRE treatment also reduced the overall soil water evaporation rate and cumulative water loss. Analysis of X-ray computed tomography (CT) scanning showed that the SRE-treated samples had a greater proportion of small pores (<60 µm). These changes were attributed mainly to SRE-stimulated microbial activities. HIGHLIGHTS: The effects of incubating a sandy soil with a synthetic root exudate (SRE) on soil physical properties and evaporation are examined.SRE incubation increased the fraction of small pores.SRE incubation increased soil penetrometer resistance and thermal conductivity.Soil hydraulic conductivity was increased in the wet region but was reduced in the dry region.SRE incubation reduced the overall evaporation rate and cumulative water loss.

Genetic mapping and genomic selection for maize stalk strength.

BACKGROUND: Maize is one of the most important staple crops and is widely grown throughout the world. Stalk lodging can cause enormous yield losses in maize production. However, rind penetrometer resistance (RPR), which is recognized as a reliable measurement to evaluate stalk strength, has been shown to be efficient and useful for improving stalk lodging-resistance. Linkage mapping is an acknowledged approach for exploring the genetic architecture of target traits. In addition, genomic selection (GS) using whole genome markers enhances selection efficiency for genetically complex traits. In the present study, two recombinant inbred line (RIL) populations were utilized to dissect the genetic basis of RPR, which was evaluated in seven growth stages. RESULTS: The optimal stages to measure stalk strength are the silking phase and stages after silking. A total of 66 and 45 quantitative trait loci (QTL) were identified in each RIL population. Several potential candidate genes were predicted according to the maize gene annotation database and were closely associated with the biosynthesis of cell wall components. Moreover, analysis of gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway further indicated that genes related to cell wall formation were involved in the determination of RPR. In addition, a multivariate model of genomic selection efficiently improved the prediction accuracy relative to a univariate model and a model considering RPR-relevant loci as fixed effects. CONCLUSIONS: The genetic architecture of RPR is highly genetically complex. Multiple minor effect QTL are jointly involved in controlling phenotypic variation in RPR. Several pleiotropic QTL identified in multiple stages may contain reliable genes and can be used to develop functional markers for improving the selection efficiency of stalk strength. The application of genomic selection to RPR may be a promising approach to accelerate breeding process for improving stalk strength and enhancing lodging-resistance.

Root growth in field-grown winter wheat: Some effects of soil conditions, season and genotype.

This work compared root length distributions of different winter wheat genotypes with soil physical measurements, in attempting to explain the relationship between root length density and soil depth. Field experiments were set up to compare the growth of various wheat lines, including near isogenic lines (Rht-B1a Tall NIL and Rht-B1c Dwarf NIL) and wheat lines grown commercially (cv. Battalion, Hystar Hybrid, Istabraq, and Robigus). Experiments occurred in two successive years under rain fed conditions. Soil water content, temperature and penetrometer resistance profiles were measured, and soil cores taken to estimate vertical profiles of pore distribution, and root number with the core-break method and by root washing. Root length distributions differed substantially between years. Wetter soil in 2014/2015 was associated with shallower roots. Although there was no genotypic effect in 2014/2015, in 2013/2014 the dwarf wheat had the most roots at depth. In the shallower layers, some wheat lines, especially Battalion, seemed better at penetrating non-structured soil. The increase in penetrometer resistance with depth was a putative explanation for the rapid decrease in root length density with depth. Differences between the two years in root profiles were greater than those due to genotype, suggesting that comparisons of different genotypic effects need to take account of different soil conditions and seasonal differences. We also demonstrate that high yields are not necessarily linked to resource acquisition, which did not seem to be limiting in the low yielding dwarf NIL.