Key message
A simple and rapid speed breeding system was developed for short-day crops that enables up to five generations per year using LED lighting systems that allow very specific adjustments ...regarding light intensity and quality.
Plant breeding is a key element for future agricultural production that needs to cope with a growing human population and climate change. However, the process of developing suitable cultivars is time-consuming, not least because of the long generation times of crops. Recently, speed breeding has been introduced for long-day crops, but a similar protocol for short-day crops is lacking to date. In this study, we present a speed breeding protocol based on light-emitting diodes (LEDs) that allow to modify light quality, and exemplarily demonstrate its effectiveness for the short-day crops soybean (
Glycine max
), rice (
Oryza sativa
) and amaranth (
Amaranthus
spp.). Adjusting the photoperiod to 10 h and using a blue-light enriched, far-red-deprived light spectrum facilitated the growth of short and sturdy soybean plants that flowered ~ 23 days after sowing and matured within 77 days, thus allowing up to five generations per year. In rice and amaranth, flowering was achieved ~ 60 and ~ 35 days after sowing, respectively. Interestingly, the use of far-red light advanced flowering by 10 and 20 days in some amaranth and rice genotypes, respectively, but had no impact on flowering in soybeans, highlighting the importance of light quality for speed breeding protocols. Taken together, our short-day crops’ speed breeding protocol enables several generations per year using crop-specific LED-based lighting regimes, without the need of tissue culture tools such as embryo rescue. Moreover, this approach can be readily applied to a multi-storey 96-cell tray-based system to integrate speed breeding with genomics, toward a higher improvement rate in breeding.
Key message
Phenotypic and genetic analysis of six spike and kernel characteristics in wheat revealed geographic patterns as well as long-term trends arising from breeding progress, particularly in ...regard to spikelet fertility, i.e. the number of kernels per spikelet, a grain yield component that appears to underlie the increase in the number of kernels per spike.
Wheat is a staple crop of global relevance that faces continuous demands for improved grain yield. In this study, we evaluated a panel of 407 winter wheat cultivars for six characteristics of spike and kernel development. All traits showed a large genotypic variation and had high heritabilities. We observed geographic patterns for some traits in addition to long-term trends showing a continuous increase in the number of kernels per spike. This breeding progress is likely due to the increase in spikelet fertility, i.e. the number of kernels per spikelet. While the number of kernels per spike and spikelet fertility were significantly positively correlated, both traits showed a significant negative correlation with thousand-kernel weight. Genome-wide association mapping identified only small- and moderate-effect QTL and an effect of the phenology loci
Rht
-
D1
and
Ppd
-
D1
on some of the traits. The allele frequencies of some QTL matched the observed geographic patterns. The quantitative inheritance of all traits with contributions of additional small-effect QTL was substantiated by genomic prediction. Taken together, our results suggest that some of the examined traits were already the basis of grain yield progress in wheat in the past decades. A more targeted exploitation of the available variation, potentially coupled with genomic approaches, may assist wheat breeding in continuing to increase yield levels globally.
Key message
This study revealed a complex genetic architecture of male floral traits in wheat, and
Rht-D1
was identified as the only major QTL. Genome-wide prediction approaches but also phenotypic ...recurrent selection appear promising to increase outcrossing ability required for hybrid wheat seed production.
Hybrid wheat breeding is a promising approach to increase grain yield and yield stability. However, the identification of lines with favorable male floral characteristics required for hybrid seed production currently poses a severe bottleneck for hybrid wheat breeding. This study therefore aimed to unravel the genetic architecture of floral traits and to assess the potential of genomic approaches to accelerate their improvement. To this end, we employed a panel of 209 diverse winter wheat lines assessed for male floral traits and genotyped with genome-wide markers as well as for
Rht
-
B1
and
Rht
-
D1
. We found the highest proportion of explained genotypic variance for the
Rht
-
D1
locus (11–24 %), for which the dwarfing allele
Rht
-
D1b
had a negative effect on anther extrusion, visual anther extrusion and pollen mass. The genome-wide scan detected only few QTL with small or medium effects, indicating a complex genetic architecture. Consequently, marker-assisted selection yielded only moderate prediction abilities (0.44–0.63), mainly relying on
Rht
-
D1
. Genomic selection based on weighted ridge-regression best linear unbiased prediction achieved higher prediction abilities of up to 0.70 for anther extrusion. In conclusion, recurrent phenotypic selection appears most cost-effective for the initial improvement of floral traits in wheat, while genome-wide prediction approaches may be worthwhile when complete marker profiles are already available in a hybrid wheat breeding program.
Soybean is a major plant protein source for both human food and animal feed, but to meet global demands as well as a trend towards regional production, soybean cultivation needs to be expanded to ...higher latitudes. In this study, we developed a large diversity panel consisting of 1503 early-maturing soybean lines and used genome-wide association mapping to dissect the genetic architecture underlying two crucial adaptation traits, flowering time and maturity. This revealed several known maturity loci, E1, E2, E3, and E4, and the growth habit locus Dt2 as causal candidate loci, and also a novel putative causal locus, GmFRL1, encoding a homolog of the vernalization pathway gene FRIGIDA-like 1. In addition, the scan for quantitative trait locus (QTL)-by-environment interactions identified GmAPETALA1d as a candidate gene for a QTL with environment-dependent reversed allelic effects. The polymorphisms of these candidate genes were identified using whole-genome resequencing data of 338 soybeans, which also revealed a novel E4 variant, e4-par, carried by 11 lines, with nine of them originating from Central Europe. Collectively, our results illustrate how combinations of QTL and their interactions with the environment facilitate the photothermal adaptation of soybean to regions far beyond its center of origin.
A modern Green Revolution gene for reduced height in wheat Würschum, Tobias; Langer, Simon M.; Longin, C. Friedrich H. ...
The Plant journal : for cell and molecular biology,
December 2017, 2017-Dec, 2017-12-00, 20171201, Letnik:
92, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Summary
Increases in the yield of wheat during the Green Revolution of the late 20th century were achieved through the introduction of Reduced height (Rht) dwarfing genes. The Rht‐B1 and Rht‐D1 loci ...ensured short stature by limiting the response to the growth‐promoting hormone gibberellin, and are now widespread through international breeding programs. Despite this advantage, interference with the plant's response to gibberellin also triggers adverse effects for a range of important agronomic traits, and consequently modern Green Revolution genes are urgently required. In this study, we revisited the genetic control of wheat height using an association mapping approach and a large panel of 1110 worldwide winter wheat cultivars. This led to the identification of a major Rht locus on chromosome 6A, Rht24, which substantially reduces plant height alone as well as in combination with Rht‐1b alleles. Remarkably, behind Rht‐D1, Rht24 was the second most important locus for reduced height, explaining 15.0% of the genotypic variance and exerting an allele substitution effect of –8.8 cm. Unlike the two Rht‐1b alleles, plants carrying Rht24 remain sensitive to gibberellic acid treatment. Rht24 appears in breeding programs from all countries of origin investigated, with increased frequency over the last decades, indicating that wheat breeders have actively selected for this locus. Taken together, this study reveals Rht24 as an important Rht gene of commercial relevance in worldwide wheat breeding.
Significance Statement
Reduced height (Rht) loci were the basis of the Green Revolution and the Rht‐B1 and Rht‐D1 semi‐dwarfing genes are now utilized globally for wheat breeding. Here, we characterize the novel Rht24 locus, show that Rht24 is of worldwide relevance and that it may be a better Green Revolution gene than those originally employed.
Key message
The phenomic predictive ability depends on the genetic architecture of the target trait, being high for complex traits and low for traits with major QTL.
Genomic selection is a powerful ...tool to assist breeding of complex traits, but a limitation is the costs required for genotyping. Recently, phenomic selection has been suggested, which uses spectral data instead of molecular markers as predictors. It was shown to be competitive with genomic prediction, as it achieved predictive abilities as high or even higher than its genomic counterpart. The objective of this study was to evaluate the performance of phenomic prediction for triticale and the dependency of the predictive ability on the genetic architecture of the target trait. We found that for traits with a complex genetic architecture, like grain yield, phenomic prediction with NIRS data as predictors achieved high predictive abilities and performed better than genomic prediction. By contrast, for mono- or oligogenic traits, for example, yellow rust, marker-based approaches achieved high predictive abilities, while those of phenomic prediction were very low. Compared with molecular markers, the predictive ability obtained using NIRS data was more robust to varying degrees of genetic relatedness between the training and prediction set. Moreover, for grain yield, smaller training sets were required to achieve a similar predictive ability for phenomic prediction than for genomic prediction. In addition, our results illustrate the potential of using field-based spectral data for phenomic prediction. Overall, our result confirmed phenomic prediction as an efficient approach to improve the selection gain for complex traits in plant breeding.
Key message
A large genetic variation, moderately high heritability, and promising prediction ability for genomic selection show that wheat breeding can substantially reduce the acrylamide forming ...potential in bread wheat by a reduction in its precursor asparagine.
Acrylamide is a potentially carcinogenic substance that is formed in baked products of wheat via the Maillard reaction from carbonyl sources and asparagine. In bread, the acrylamide content increases almost linearly with the asparagine content of the wheat grains. Our objective was, therefore, to investigate the potential of wheat breeding to contribute to a reduction in acrylamide by decreasing the asparagine content in wheat grains. To this end, we evaluated 149 wheat varieties from Central Europe at three locations for asparagine content, as well as for sulfur content, and five important quality traits regularly assessed in bread wheat breeding. The mean asparagine content ranged from 143.25 to 392.75 mg/kg for the different wheat varieties, thus underlining the possibility to reduce the acrylamide content of baked wheat products considerably by selecting appropriate varieties. Furthermore, a moderately high heritability of 0.65 and no negative correlations with quality traits like protein content, sedimentation volume and falling number show that breeding of quality wheat with low asparagine content is feasible. Genome-wide association mapping identified few QTL for asparagine content, the largest explaining 18% of the genotypic variance. Combining these QTL with a genome-wide prediction approach yielded a mean cross-validated prediction ability of 0.62. As we observed a high genotype-by-environment interaction for asparagine content, we recommend the costly and slow laboratory analysis only for late breeding generations, while selection in early generations could be based on marker-assisted or genomic selection.
Summary
Winter hardiness is important for the adaptation of wheat to the harsh winter conditions in temperate regions and is thus also an important breeding goal. Here, we employed a panel of 407 ...European winter wheat cultivars to dissect the genetic architecture of winter hardiness. We show that copy number variation (CNV) of CBF (C‐repeat Binding Factor) genes at the Fr‐A2 locus is the essential component for winter survival, with CBF‐A14 CNV being the most likely causal polymorphism, accounting for 24.3% of the genotypic variance. Genome‐wide association mapping identified several markers in the Fr‐A2 chromosomal region, which even after accounting for the effects of CBF‐A14 copy number explained approximately 15% of the genotypic variance. This suggests that additional, as yet undiscovered, polymorphisms are present at the Fr‐A2 locus. Furthermore, CNV of Vrn‐A1 explained an additional 3.0% of the genotypic variance. The allele frequencies of all loci associated with winter hardiness were found to show geographic patterns consistent with their role in adaptation. Collectively, our results from the candidate gene analysis, association mapping and genome‐wide prediction show that winter hardiness in wheat is a quantitative trait, but with a major contribution of the Fr‐A2 locus.
Significance statement
Copy number variation (CNV) in the human genome has been associated with diseases, but little is known about CNV in crops. Here, we used a panel of over 400 winter wheat cultivars to dissect the genetic architecture of winter hardiness. We show that CNV at the Fr‐A2 locus, which is composed of a cluster of CBF genes that are upregulated in response to low temperatures, contributes substantially to winter hardiness in wheat. The allele frequencies of all loci associated with winter hardiness showed geographic patterns consistent with their role in adaptation.
Phosphorus (P) is an essential macronutrient for plants, but also a limited resource worldwide. Strict regulations for fertilizer applications in the European Union are a consequence of the negative ...environmental effects in case of improper use. Maize is typically grown with the application of P starter fertilizer, which, however, might be reduced or even omitted if suitable varieties were available. This study was performed with the 20 commercially most important maize hybrids in Germany evaluated in multi-location field trials with the aim to investigate the potential to breed for high-performing maize hybrids under reduced P starter fertilizer. At the core location, three starter fertilizers with either phosphate (triple superphosphate, TSP), ammonium nitrate (calcium ammonium nitrate, CAN), or a combination of ammonium and phosphate (diammonium phosphate, DAP) were evaluated relative to a control and traits from youth development to grain yield were assessed. Significant differences were mainly observed for the DAP starter fertilizer, which was also reflected in a yield increase of on average +0.67 t/ha (+5.34%) compared to the control. Correlations among the investigated traits varied with starter fertilizer, but the general trends remained. As expected, grain yield was negatively correlated with grain P concentration, likely due to a dilution effect. Importantly, the genotype-by-starter fertilizer interaction was always non-significant in the multi-location analysis. This indicates that best performing genotypes can be identified irrespective of the starter fertilizer. Taken together, our results provide valuable insights regarding the potential to reduce starter fertilizers in maize cultivation as well as for breeding maize for P efficiency under well-supplied conditions.
Key message
Restoration of fertility in the cytoplasmic male sterility-inducing
Triticum timopheevii
cytoplasm can be achieved with the major restorer locus
Rf3
located on chromosome 1B, but is also ...dependent on modifier loci.
Hybrid breeding relies on a hybrid mechanism enabling a cost-efficient hybrid seed production. In wheat and triticale, cytoplasmic male sterility based on the
T. timopheevii
cytoplasm is commonly used, and the aim of this study was to dissect the genetic architecture underlying fertility restoration. Our study was based on two segregating F
2
triticale populations with 313 and 188 individuals that share a common female parent and have two different lines with high fertility restoration ability as male parents. The plants were cloned to enable replicated assessments of their phenotype and fertility restoration was evaluated based on seed set or staining for pollen fertility. The traits showed high heritabilities but their distributions differed between the two populations. In one population, a quarter of the lines were sterile, conforming to a 3:1 segregation ratio. QTL mapping identified two and three QTL in these populations, with the major QTL being detected on chromosome 1B. This QTL was collinear in both populations and likely corresponds to
Rf3
. We found that
Rf3
explained approximately 30 and 50% of the genotypic variance, has a dominant mode of inheritance, and that the female parent lacks this locus, probably due to a 1B.1R translocation. Taken together,
Rf3
is a major restorer locus that enables fertility restoration of the
T. timopheevii
cytoplasm, but additional modifier loci are needed for full restoration of male fertility. Consequently,
Rf3
holds great potential for hybrid wheat and triticale breeding, but other loci must also be considered, either through marker-assisted or phenotypic selection.
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