Construction of a novel Wheat 55 K SNP array-derived genetic map and its utilization in QTL mapping for grain yield and quality related traits

Wheat is one of the most important staple crops for supplying nutrition and energy to people world. A new genetic map based on the Wheat 55 K SNP array was constructed using recombinant inbred lines derived from a cross between Zhongkemai138 and Kechengmai2 to explore the genetic foundation for wheat grain features. This new map covered 2,155.72 cM across the 21 wheat chromosomes with 11,455 markers. And 2,846 specific markers for this genetic map and 148 coincident markers among different maps were documented, which was helpful for improving and updating wheat genetic and genomic information. Using this map, a total of 68 additive QTLs and 82 pairs of epistatic QTLs were detected for grain features including yield, nutrient composition, and quality-related traits by QTLNetwork 2.1 and IciMapping 4.1 software. Fourteen additive QTLs and one pair of epistatic QTLs could be detected by both software programs and thus regarded as stable QTLs here, all of which explained higher phenotypic variance and thus could be utilized for wheat grain improvement. Additionally, thirteen additive QTLs were clustered into three genomic intervals (C4D.2, C5D, and C6D2), each of which had at least two stable QTLs. Among them, C4D.2 and C5D have been attributed to the famous dwarfing gene Rht2 and the hardness locus Pina, respectively, while endowed with main effects on eight grain yield/quality related traits and epistatically interacted with each other to control moisture content, indicating that the correlation of involved traits was supported by the pleotropic of individual genes but also regulated by the gene interaction networks. Additionally, the stable additive effect of C6D2 (QMc.cib-6D2 and QTw.cib-6D2) on moisture content was also highlighted, potentially affected by a novel locus, and validated by its flanking Kompetitive Allele-Specific PCR marker, and TraesCS6D02G109500, encoding aleurone layer morphogenesis protein, was deduced to be one of the candidate genes for this locus. This result observed at the QTL level the possible contribution of grain water content to the balances among yield, nutrients, and quality properties and reported a possible new locus controlling grain moisture content as well as its linked molecular marker for further grain feature improvement.

Tall 3-dwarfs: oxymoron or opportunity to increase grain yield in sorghum?

Plant height was positively correlated with grain yield across a large set of 3-dwarf sorghum hybrids and production environments in north-eastern Australia. In industrialised countries, plant breeders tend to select for short plant stature in cereals like wheat, barley and rice, but also grain sorghum. This is mainly to prevent stalk lodging and to allow for machine harvesting. However, this counteracts an intrinsic positive relationship between plant height and yield potential often observed in cereals. We used data from multi-environment breeding trials comprising large sets of female sorghum lines from a range of pedigrees in hybrid combination with five different male testers. The hybrids were grown in 22 different rainfed environments in north-eastern Australia, which allowed us to thoroughly examine the relationship between plant height and yield across a range of productivity levels. Covariate analysis showed that in 38 out of the 90 tested relationships, grain yield was significantly (p < 0.05) positively and in only one case significantly negatively associated with plant height. This strong positive association between the traits was supported by the observation that 87% of the effects were either positive or zero. The effects of height on yield ranged from a decrease of 0.015 t ha^-1 to an increase of 0.057 t ha^-1 cm^-1. The majority of the negative effects were observed in low-yielding trials and the positive effect of height tended to increase with increasing mean trial yield. Opportunities to increase yield potential by selecting for slightly taller sorghum hybrids therefore need to be explored in context with the target environments and in combination with other means to control the risks of lodging.

The Allelic Diversity of the Gibberellin Signaling Pathway Genes in Aegilops tauschii Coss

Gibberellin-insensitive reduced height genes are widely spread in modern wheat varieties, making them resistant to lodging under conditions of intensive farming. However, the limited diversity of these genes present in wheat germplasm can limit the adaptability of newly created cultivars to the changing climate. The diversity of the gibberellin signaling pathway genes involved in plant height control- Reduced height 1 (Rht-D1), Gibberellin-insensitive dwarf 1 (Gid1‑D) and Gibberellin-insensitive dwarf 2 (Gid2-D)-was studied in the diploid wild goatgrass Aegilops tauschii Coss., one of the ancestral species of the bread wheat (Triticum aestivum L.) and the donor of its D subgenome, using high-throughput sequencing. The examination of 24 Ae. tauschii accessions of different geographical origins revealed a large number of new alleles (haplotypes) not found in bread wheat varieties. Some of the detected polymorphisms lead to changes in the amino acid sequence of proteins. Four isoforms (amino acid sequence variants) were found for the RHT-D1 protein, and two isoforms-for the GID1 and GID2 proteins, each. An analysis of the co-occurrence frequencies of various isoforms of the three proteins showed that their combinations were not random in Ae. tauschii, which may indicate the functional significance of their differences. New alleles of the Rht-D1, Gid1-D, and Gid2-D genes are promising for introgression into bread wheat and studying their effect on plant height and adaptability.

Breeding for dual-purpose wheat varieties using marker-trait associations for biomass yield and quality traits

This study demonstrates that an active breeding nursery with rotation can be used to identify marker-trait associations for biomass yield and quality parameters that are important for biorefinery purposes. Wheat straw is a valuable feedstock for bioethanol production, but due to the recalcitrant nature of lignocellulose, its efficient use in biorefineries is limited by its low digestibility and difficult conversion of structural carbohydrates into free sugars. A genome-wide association study (GWAS) was conducted to search for significant SNP markers that could be used in a breeding programme to improve the value of wheat straw in a biorefinery setting. As part of a 3-year breeding programme (2013-2016), 190 winter wheat lines were phenotyped for traits that affect the yield and quality of the harvested biomass. These traits included straw yield, plant height, lodging at three growth stages and Septoria tritici blotch (STB) susceptibility. Release of glucose, xylose and arabinose was determined after hydrothermal pretreatment and enzymatic hydrolysis of the straw. The lines were genotyped using 15 K SNP markers and 5552 SNP markers could be used after filtering. Heritability for all traits ranged from 0.02 to 0.74. GWASs were conducted using CMLM, SUPER and FarmCPU algorithms, to analyse which algorithm could detect the highest number of marker-trait associations (MTAs). Comparable tendencies were obtained from CMLM and FarmCPU, but FarmCPU produced the most significant results. MTAs were obtained for lodging, harvest index, plant height, STB, glucose, xylose and arabinose at a significance level of p < 9.01 × 10^-6. MTAs in chromosome 6A were observed for glucose, xylose and arabinose, and could be of importance for increasing sugar release for bioethanol production.

The Impact of the Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development Under Field Conditions

The Reduced Height (Rht) genes formed the basis for the green revolution in wheat by decreasing plant height and increasing productive tillers. There are two current widely used Rht mutant alleles, Rht-B1b and Rht-D1b. Both reduce plant height by 20% and increase seed yield by 5-10%. They are also associated with decreased seed size and protein content. Here, we tested the degree to which Rht-B1b impacts flag leaf photosynthetic rates and carbon and nitrogen partitioning to the flag leaf and grain during grain fill under field conditions using near isogenic lines (NILs) that were either standard height (Rht-B1a) or semi-dwarf (Rht-B1b). The results demonstrate that at anthesis, Rht-B1b reduces flag leaf photosynthetic rate per unit area by 18% and chlorophyll A content by 23%. Rht-B1b significantly reduced grain protein beginning at 14 days post anthesis (DPA) with the greatest difference seen at 21 DPA (12%). Rht-B1b also significantly decreased individual seed weight beginning at 21 DPA and by 15.2% at 28 DPA. Global expression analysis using RNA extracted from developing leaves and stems demonstrated that genes associated with carbon and nitrogen metabolism are not substantially altered by Rht-B1b. From this study, we conclude that Rht-B1b reduces flag leaf photosynthetic rate at flowering while changes in grain composition begin shortly after anthesis.

Raising yield potential of wheat. III. Optimizing partitioning to grain while maintaining lodging resistance

A substantial increase in grain yield potential is required, along with better use of water and fertilizer, to ensure food security and environmental protection in future decades. For improvements in photosynthetic capacity to result in additional wheat yield, extra assimilates must be partitioned to developing spikes and grains and/or potential grain weight increased to accommodate the extra assimilates. At the same time, improvement in dry matter partitioning to spikes should ensure that it does not increase stem or root lodging. It is therefore crucial that improvements in structural and reproductive aspects of growth accompany increases in photosynthesis to enhance the net agronomic benefits of genetic modifications. In this article, six complementary approaches are proposed, namely: (i) optimizing developmental pattern to maximize spike fertility and grain number, (ii) optimizing spike growth to maximize grain number and dry matter harvest index, (iii) improving spike fertility through desensitizing floret abortion to environmental cues, (iv) improving potential grain size and grain filling, and (v) improving lodging resistance. Since many of the traits tackled in these approaches interact strongly, an integrative modelling approach is also proposed, to (vi) identify any trade-offs between key traits, hence to define target ideotypes in quantitative terms. The potential for genetic dissection of key traits via quantitative trait loci analysis is discussed for the efficient deployment of existing variation in breeding programmes. These proposals should maximize returns in food production from investments in increased crop biomass by increasing spike fertility, grain number per unit area and harvest index whilst optimizing the trade-offs with potential grain weight and lodging resistance.

Competing effects of buckling and anchorage strength on optimal wheat stalk geometry

We seek the ideal wheat stalk, which minimizes the structural mass required to support a fixed grain load in the presence of gravity and wind. The optimization search is restricted to stepped cylindrical stems of known moduli and density but unknown dimension. Stem buckling and root anchorage strength are assumed to place restrictions on the permissible stalk resonant frequency in the presence of a specified wind forcing frequency. These effects are described mathematically, and the penalty parameter method is used to find stem mass minima for various stalk heights. In general, there are two alternative solution branches. The lower solution is the global minimum but it is probably impractical for field crops exposed to natural wind. The upper minimum is more conservative and therefore requires more stem mass. Due to the competing requirements of buckling versus anchorage strength, the parameter study shows that optimal wheat stem geometry has a nonlinear dependence on the intensity of gravity and the frequency spectra of the wind.

Relative safety factors against global buckling, anchorage rotation, and tissue rupture in wheat

The objective of this study was to quantify the effect of specific physical and biological factors on the relative likelihood of biomechanical failure in wheat. Wind-related crop damage is a major obstacle to wheat production that costs several billion dollars per year. The four factors varied in this study were breeding line, dwarfing gene dose, soil type, and fertilization. A theoretical model describing the dynamic structural response of living plants was used to define margins of safety against global buckling, anchorage rotation, and tissue rupture. These relative safety factors were defined for each treatment in comparison with a tall wheat variety selected from a breeding line called Seri and grown in sandy soil with low fertilization. Compared to this reference, the relative safety factor against global buckling was increased (+39%, p<0.01), and the relative safety factor against anchorage rotation was decreased (-11%, p<0.025), by one allele of the dwarfing gene. The relative safety factor against tissue rupture was unaffected by the dwarfing gene but was consistently lower (-26%, p<0.01) in a second breeding line called Kauz. Soil type and fertility did not affect the relative safety factors and this negative finding was significant at p<0.05. The key finding was that the strength of wheat was affected more by genetic rather than by environmental factors, which suggests that some varieties are intrinsically more robust than others. Also, the relative safety factor against anchorage rotation was inversely proportional to the relative safety factor against buckling, which suggests that there are competing constraints on the dynamic structural behavior of wheat.

Avenues for genetic modification of radiation use efficiency in wheat

Radiation use efficiency (RUE) of a crop is a function of several interacting physiological phenomena, each of which can be tackled independently from the point of view of genetic improvement. Although wheat breeding has not raised RUE substantially, theoretical calculations suggest room for improvement. Selection for higher rates of leaf photosynthesis at saturating light intensities (Amax) has not resulted in improved RUE of crops, perhaps in part because most leaves in a canopy are not light-saturated. However, higher Amax may be observed as a pleiotropic effect of other yield-enhancing genes (e.g. genes for reduced height). Genetic transformation of Rubisco to double its specificity for CO2 would theoretically increase Amax by perhaps 20%, and some evidence suggests that photosynthesis at sub-saturating light intensities would also be improved. However, photo-protection may be jeopardized if capacity for oxygenase activity is impaired. Photosynthetic rate of the whole eanopy can be enhanced by manipulation of leaf angle, which is under relatively simple genetic control, and possibly by manipulating leaf-N distribution throughout the canopy. Genetic diversity for adaptation of lower canopy leaves (e.g. changes in chlorophyll a:b ratio) to reduced light intensity observed in some crops needs to be investigated in wheat. Improved RUE may be achieved by increasing sink demand (i.e. kernel number) if excess photosynthetic capacity exists during grain filling, as suggested by a number of studies in which source-sink balance was manipulated. Some evidence suggests that improved sink strength may be achieved by lengthening the duration of the period for juvenile spike growth. Balancing source- and sink-strength is a complex genetic challenge since a crop will change between source and sink limitation as conditions vary during the day, and with phenological stage. Improved RUE will be partly a function of a genotype's ability to buffer itself against changes in its environment to match the demand imposed by its development. Analysis of the physiological basis of genotype by environment interactions may indicate avenues for genetic improvement. The genetic control of photosynthetic regulation may be elucidated in the future through the application of genomics. However, given a lack of specific knowledge on the genetic basis of RUE, empirical selection is currently the most powerful tool for detecting favourable genetic interactions resulting from crosses between lines with superior photosynthetic traits and other high yielding characteristics. Selection for superior segregants can be accelerated using rapidly measured physiological selection traits, such as stomatal conductance or canopy temperature depression.