Soybean plant height QTL mapping and meta‐analysis for mining candidate genes

Plant height is closely related to seed yield of soybean. The goal of this study was to identify important loci affecting soybean plant height using meta‐analysis based on a reference physical map. Plant height related to QTLs was mapped across eight years with a RIL population by WinQTLCart v2.5. 182 QTLs related to plant height of soybean from database and our research were collected, and each QTL was projected onto the soybean physical map by software BioMercator v2.1. The confidence interval of meta‐QTL ranged from 0.09 to 5.07 Mb, and the mean phenotypic variance ranged from 4.9% to 73.0%. Furthermore, 4,259 candidate genes were located in these consensus QTLs, and 40 of them were involved in the plant growth and stem elongation and annotated as plant hormone signal transduction (pathway ID ko04075) in KEGG pathway. These results would lay a foundation for fine mapping of QTLs/genes related to plant height and marker‐assisted selection for breeding in soybean.     

Genetic divergence in two tropical maize composites after four cycles of reciprocal recurrent selection

Two tropical maize composites were subjected to four cycles of reciprocal recurrent selection to develop divergent inbred lines with good combining ability. This study was conducted to examine the extent of genetic diversity, changes in allele composition and genetic structure, of 100 randomly selected S₁ lines each from the original (C₀) and advanced (C₄) selection cycles of TZL COMP3 and TZL COMP4, genotyped using single nucleotide polymorphism (SNP) markers. Results revealed that the proportion of alleles at both low and high frequencies decreased from C₀ to C₄, whereas those at intermediate frequencies increased at C₄ in the two composites. More unique and other alleles were lost at C₄ in TZL COMP3 relative to those in TZL COMP4. The changes in different measures of genetic diversity were either small or negligible with selection in the two composites. The proportion of markers departing from Hardy–Weinberg equilibrium (HWE) decreased with selection, whereas the total number of pairs of markers in linkage disequilibrium increased with selection in the two composites. Examination of changes in population structures using a model‐based approach as well as cluster and multivariate analyses found a high degree of concordance in stratifying the 400 S₁ lines into four non‐overlapping groups corresponding to the two selection cycles each within the reciprocal composites. The observed molecular‐based divergence between cycles within the same composite and the clear differentiation between the complementary composites highlight the importance of reciprocal recurrent selection for preserving genetic diversity for long‐term selection. This increases the potential of the advanced selection cycles to sustain genetic gain in productivity of hybrids adapted to the savannas in West and Central Africa.     

Migration strategies of brown trout (Salmo trutta) in a subarctic river system as revealed by stable isotope analysis

We estimated the proportions of anadromous and freshwater‐resident brown trout (Salmo trutta) in different parts of the subarctic River Näätämöjoki/Neidenelva system (Finland and Norway) using carbon, nitrogen and hydrogen stable isotope analyses of archived scales as identifiers of migration strategy. Our results showed that carbon stable isotope values were the best predictor of migration strategy. Most individuals fell into two clearly distinct groups representing anadromous (47%) or freshwater‐resident (42%) individuals, but some fish had intermediate carbon values suggesting repeated movement between freshwater and the sea. The proportion of anadromous individuals decreased steadily with distance from the sea forming a spatial continuum in migration strategies which is probably maintained by the combination of several factors such as divergent availability of food resources, variable migration costs and genetic differences. These within‐catchment differences in migration strategies should be taken into account in fisheries management practices.     

Genomic prediction for yields,processing and nutritional quality traits in cultivated potato (Solanum tuberosum L.)

Current potato breeding approaches are hampered by several factors including costly seed tubers, tetrasomic inheritance and inbreeding depression. Genomic selection (GS) demonstrated interesting results regardless of the ploidy level, and can be harnessed to circumvent these problems. In this work, three GS models were evaluated using 50,107 informative SilicoDArT markers and 11 traits in two values for cultivation and use (VCU) potato trials. Two key breeding problems modelled included predicting the performance of (i) new and unphenotyped clones (cross‐validation) and (ii) a VCU using another as training set (TS). GS models performed comparably. Cross‐validation accuracy was high for D35, D45, DMW and BVAL, in ascending order. Prediction accuracies of the VCUs were highly correlated, but the best prediction was obtained for the smaller VCU using the bigger as TS. Cross‐validation and VCU prediction accuracies were higher when bigger TSs were used. The findings herein indicate that GS can be attractively integrated in potato breeding, particularly in early clonal generations to predict and select for traits with low heritability which would otherwise require more testing years, environments and resources.     

Development of a kompetitive allele‐specific PCR marker for selection of the mutated Wx‐D1d allele in wheat breeding

Waxy (Wx) protein is a key enzyme for synthesis of amylose in endosperm. Amylose content in wheat grain influences the quality of end‐use products. Seven alleles have been described at the Wx‐D1 locus, but only two of them (Wx‐D1b, Wx‐D1e) were genotyped with codominant markers. The waxy wheat line K107Wx1 developed by treating ‘Kanto 107’ seeds with ethyl methanesulphonate carries the Wx‐D1d allele. However, no molecular basis supports this nomenclature. In the present study, DNA sequence analysis confirmed that a single nucleotide polymorphism in the sixth exon of Wx‐D1 changed tryptophan at position 301 into a termination codon. Based on this sequence variation, a PCR‐based KASP marker was developed to detect this point mutation using 68 BC₈F₁ plants and 297 BC₈F₂ lines derived from the cross ‘Ningmai 14’*9/K107Wx1. Combined with codominant markers for the Wx‐A1 and Wx‐B1 alleles, waxy and non‐waxy near‐isogenic lines were distinguished. The KASP marker was efficient in identifying the mutant allele and can be used to transfer waxiness to elite lines.     

Short‐term releases of CO2 from newly mixed biochar and calcareous soil

The work aimed to quantify native organic C mobilized in one calcareous soil in the 21 days after addition of biochar at a range of large to very large applications. The experiment was carried out in unplanted microcosms, and CO₂ flux was used as a measure of net mineralization. A rapid methodological approach, which does not require ¹³C as a tracer, was used to assess any priming effects induced by the biochar. The amount of CO₂‐C mobilized was small relative to the amount of biochar C and proportional to the amount of the biochar added. The additional CO₂‐C was similar to the content of the water‐soluble organic carbon in the biochar added with each application. No interaction with native soil C, that is priming effect, was observed.     

Soil organic carbon stock variability in the Northern Gangetic Plains of India: interaction between agro‐ecological characteristics and cropping systems

Soil organic carbon (SOC) content and its spatial distribution in the Northern Gangetic Plain (NGP) Zone of India were determined to establish the cause–effect relationship between agro‐ecological characteristics, prevailing crop management practices and SOC stock. Area Spread Index (ASI) approach was used to collect soil samples from the NGP areas supporting predominant cropping systems. Exponential ordinary kriging was found most suitable geo‐statistical model for developing SOC surface maps of the NGP. Predicted surface maps indicated that 43.7% area of NGP had 0.5–0.6% SOC, while the rest of the area was equally distributed with high (0.61–0.75%) and low (< 0.5%) SOC content levels. Averaged across cropping systems, maximum SOC content was recorded in Bhabar and Tarai Zone (BTZ), followed by Central Plain Zone (CPZ), Mid‐Western Plain Zone (MWPZ), Western Plain Zone (WPZ) and South‐Western Plain Zone (SWPZ) of the NGP. The SOC stock was above the optimum threshold (> 12.5 Mg/ha) in 97.8, 57.6 and 46.4% areas of BTZ, CPZ and MWPZ, respectively. Only 9.8 and 0.4% area of WPZ and SWPZ, respectively, had SOC stock above the threshold value. The variation in SOC stock was attributed largely to carbon addition through recycling of organic sources, cropping systems, tillage intensity, crop or residue cover and land‐use efficiency, nutrient‐use pattern, soil texture and prevailing ecosystem. Adoption of conservation agriculture, balanced use of nutrients, inclusion of legumes in cropping systems and agro‐forestry were suggested for enhancing SOC stock in the region.     

Management of yellow dwarf disease in Europe in a post‐neonicotinoid agriculture

Barley/cereal yellow dwarf viruses (YDVs) cause yellow dwarf disease (YDD), which is a continuous risk to cereals production worldwide. These viruses cause leaf yellowing and stunting, resulting in yield reductions of up to 80%. YDVs have been a consistent but low‐level problem in European cereal cultivation for the last three decades, mostly due to the availability of several effective insecticides (largely pyrethroids and more recently neonicotinoids) against aphid vectors. However, this has changed recently, with many insecticides being lost, culminating in a recent European Union (EU) regulation prohibiting outdoor use of the neonicotinoid‐insecticide compounds. This change is coupled with the growing challenge of insecticide‐resistant aphids, the lack of genetic resources against YDVs, and a knowledge deficit around the parameters responsible for the emergence and spread of YDD. This means that economic sustainability of cereal cultivation in several European countries including France and United Kingdom is now again threatened by this aphid‐vectored viral disease. In this review, we summarize the current knowledge on the YDV pathosystem, describe management options against YDD, analyse the impacts of the neonicotinoid ban in Europe, and consider future strategies to control YDV. © 2020 Society of Chemical Industry