Alfalfa (M. sativa L.) is a highly valuable forage crop, providing >58 Mt of hay, silage, and pasture each year in the United States. As alfalfa is an outcrossing autotetraploid crop, however, breeding for enhanced agronomic traits is challenging and progress has historically not been rapid. Methods that make use of genotypic information and statistical models to generate a genomic estimated breeding value (GEBV) for each plant at a young age hold a great deal of promise to accelerate breeding gains. An emerging genomic breeding pipeline employs SNP chips or genotyping-by-sequencing (GBS) to identify SNP markers in a training population, followed by the use of a statistical model to find associations between the discovered SNPs and traits of interest, followed by genomic selection (GS), a breeding program utilizing the trained model to predict breeding values and making selections based on the estimated breeding value (EBV). Much work has been done in recent years in all of these areas, to generate marker sets and discover SNPs associated with desirable traits, and the application of these technologies in alfalfa breeding programs is under way. However, GBS/GWAS/GS is still a new breeding paradigm, and work is ongoing to evaluate different models, software, and methods for use in such programs. In this review, we look at the progress of alfalfa genomics over the past half-decade, and review work comparing models and methods relevant to this new type of breeding strategy.

To evaluate the effects of various rotation systems on rice grain yield and N use efficiency, a paddy-upland cropping experiment (2013-2016) was conducted in southeastern China. The experiment was designed using six different rice--winter crop rotations: rice-fallow (RF), rice-wheat (RW), rice-potato with rice straw mulch (RP), rice-green manure (Chinese milk vetch; RC-G), rice-oilseed rape (RO), and rice-green manure crop (oilseed rape with fresh straw incorporated into soil at flowering; RO-G) and three N rates, N0 (0?kg?N?ha⁻¹), N1 (142.5?kg?N?ha⁻¹), and N2 (202.5?kg?N?ha⁻¹). Average rice yields in the RF (5.93?t?ha⁻¹) rotation were significantly lower than those in the rotations with winter crops (7.20-7.48?t?ha⁻¹) under the N0 treatment, suggesting that incorporation of straw might be more effective for increasing soil N than winter fallow. The rice yield differences among the rotations varied by year with the N input. In general, the grain yields in the RP and RO-G rotations -were respectively 11.6-28.5% and 14.80-37.19% higher than those in the RF in plots with N applied. Increasing the N rate may have tended to minimize the average yield gap between the RF and the other rotations; the yield gaps were 18.55%, 4.14%, and 0.23% in N0, N1, and N2, respectively. However, the N recovery efficiency in the RF was significantly lower than that in other rotations, except for 2015 under both N1 and N2 rates, a finding that implies a large amount of chemical N loss. No significant differences in nitrogen agronomic efficiency (NAE) and physiological efficiency (NPE) were found between the rotations with legume (RC-G) and non-legume (RO and RW) winter crops, a result that may be due partly to straw incorporation. For this reason, we concluded that the return of straw could reduce differences in N use efficiency between rotations with and without legume crops. The degree of synchrony between the crop N demand and the N supply was evaluated by comparison of nitrogen balance degree (NBD) values. The NBD values in the RP and RW were significantly lower than those in the other rotations under both N1 and N2 rates. Thus, in view of the higher grain yield in the RP compared to the RW under the N1 rate, the RP rotation might be a promising practice with comparable grain yield and greater N use efficiency under reduced N input relative to the other rotations. The primary yield components of the RF and RP were identified as number of panicles m⁻² and numbers of kernels panicle⁻¹, respectively. The NAE and NPE were positively correlated with harvest index, possibly providing a useful indicator for evaluating N use efficiency.

An understanding of wheat yield and yield stability response to fertilization is important for sustainable wheat production. A 36-year long-term fertilization experiment was employed to evaluate the yield and yield stability of winter wheat. Five fertilization regimes were compared, including (1) CK, no fertilizer; (2) NPK, inorganic fertilizer only; (3) O, organic fertilizer only; (4) NPKO, 50% of NPK plus 50% of O, and (5) HNPKO, 80% of NPK plus 80% of O. The greatest yield increase was recorded in HNPKO, followed by NPKO, with O producing the lowest mean yield increase. Over the 36?years, the rate of wheat yield increase in fertilized plots ranged from 95.31?kg?ha⁻¹?year⁻¹ in the HNPKO to 138.65?kg?ha⁻¹?year⁻¹ in the O. Yield stability analysis using the additive main effects and multiplicative interactions (AMMI) method assigned 62.3%, 26.3%, and 11.4% of sums of squares to fertilization effect, environmental effect, and fertilization?×?environment interaction effect, respectively. The combination of inorganic and organic fertilization (NPKO and HNPKO) appeared to produce more stable yields than O or NPK, with lower coefficients of variation and AMMI stability value. However, wheat grown with O seemed to be the most susceptible to climate change and the least productive among the fertilized plots. Significant correlations of grain yield with soil properties and with mean air temperature were observed. These findings suggest that inorganic?+?organic fertilizer can increase wheat yield and its stability by improvement in soil fertility and reduction in variability to climate change.

Wheat (Triticum aestivum L.) is one of the three major global food crops. High-temperature stress can affect its yield and quality. Studies of the effect of high-temperature stress on wheat kernel development are important because they can reveal the stability of wheat quality and lead to the genetic improvement of wheat quality traits. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) method was adopted to analyze changes in the protein expression profile of wheat cultivars under high temperature stress. The protein content of wheat grain increased under heat stress, while the SDS-sedimentation value and starch content decreased. Grain filling was deficient under high temperature stress, which reduced thousand-kernel weight but did not affect wheat kernel length. The 207 differentially expressed proteins identified in Gaocheng 8901 under heat stress were associated with energy metabolism, growth and development, and stress response. Gene Ontology enrichment analysis showed that the annotated proteins that were differentially expressed in Gaocheng 8901 under heat stress were involved mainly in stimulus response, abiotic stress response, stress response, and plasma membrane. A set of 78 differentially expressed proteins were assigned to 83 KEGG signaling/metabolic pathways. KEGG pathway enrichment analysis showed that this set of proteins was significantly enriched in members of 51 pathways, and the proteins participated mainly in protein synthesis in the endoplasmic reticulum, starch and sucrose metabolism, and reaction on ribosomes. Five differentially expressed proteins were involved in protein-protein interaction networks that may greatly influence the yield and quality of wheat grain. In wheat, high-temperature stress leads to a variety of effects on protein expression and may ultimately cause changes in yield and quality.

Drought stress is one of the main factors limiting yield in tea plants. The plant cell's ability to preserve K⁺ homeostasis is an important strategy for coping with drought stress. Plasma membrane H⁺-ATPase in the mesophyll cell is important for maintaining membrane potential to regulate K⁺ transmembrane transport. However, no research to date has investigated the possible relationship between plasma membrane H⁺-ATPase and mesophyll K⁺ retention in tea plants under drought and subsequent rehydration conditions. In our experiment, drought stress inhibited plasma membrane H⁺-ATPase activities and induced net H⁺ influx, leading to membrane potential depolarization and inducing a massive K⁺ efflux in tea plant mesophyll cells. Subsequent rehydration increased plasma membrane H⁺-ATPase activity and induced net H⁺ efflux, leading to membrane potential hyperpolarization and thus lowering K⁺ loss. A first downregulated and then upregulated plasma membrane H⁺-ATPase protein expression level was also observed under drought and subsequent rehydration treatment, a finding in agreement with the change of measured plasma membrane H⁺-ATPase activities. Taken together, our results suggest that maintenance of mesophyll K⁺ in tea plants under drought and rehydration is associated with regulation of plasma membrane H⁺-ATPase activity.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most devastating diseases of common wheat (Triticum aestivum L.). The wheat line 92145E8-9 is immune to Bgt isolate E09. Genetic analysis reveals that the powdery mildew resistance in 92145E8-9 is controlled by a single dominant gene, temporarily designated Ml92145E8-9. Bulked-segregant analysis (BSA) with simple sequence repeat (SSR) markers indicates that Ml92145E8-9 is located on chromosome 2AL. According to the reactions of 92145E8-9, VPM1 (Pm4b carrier), and Lankao 906 (PmLK906 carrier) to 14 Bgt isolates, the resistance spectrum of 92145E8-9 differs from those of Pm4b and PmLK906, both of which were previously localized to 2AL. To test the allelism among Ml92145E8-9, Pm4b and PmLK906, two F₂ populations of 92145E8-9?×?VPM1 (Pm4b) and 92145E8-9?×?Lankao 906 (PmLK906) were developed in this study. Screening of 784 F₂ progeny of 92145E8-9?×?VPM1 and 973 F₂ progeny of 92145E8-9?×?Lankao 906 for Bgt isolate E09 identified 37 and 19 susceptible plants, respectively. These findings indicated that Ml92145E8-9 is non-allelic to either Pm4b or PmLK906. Thus, Ml92145E8-9 is likely to be a new powdery mildew resistance gene on 2AL. New polymorphic markers were developed based on the collinearity of genomic regions of Ml92145E8-9 with the reference sequences of the International Wheat Genome Sequencing Consortium (IWGSC). Ml92145E8-9 was mapped to a 3.6?cM interval flanked by molecular markers Xsdauk13 and Xsdauk682. This study also developed five powdery mildew-resistant wheat lines (SDAU3561, SDAU3562, SDAU4173, SDAU4174, and SDAU4175) using flanking marker-aided selection. The markers closely linked to Ml92145E8-9 would be useful in marker-assisted selection for wheat powdery mildew resistance breeding.

A new, improved version of the catalog of 182 alleles at the six Gli loci of common wheat (T. aestivum L.) shown in electrophoregrams of 128 standard genotypes was used for analysis of 1060 cultivars and lines bred in the 20th century. The most frequent alleles in the studied germplasm occurred with frequencies of 18%-40%, with 30 unique alleles, one in each cultivar. Extremely high genetic diversity was found (average H for the six main Gli loci was 0.870 ± 0.046), nearly identical in winter (H = 0.831) and spring (H = 0.856) wheats but differing among 28 groups of cultivars released in 22 countries. Each country or region was characterized by its own specific set of the most frequent Gli alleles, and the 28 cultivar groups formed five main relationship clusters if polymorphism at the six Gli loci was considered. However, different levels of similarity between groups of cultivars were found if polymorphism of the A, B, or D genomes of common wheat was tested separately. In general, the 20th century germplasm of common wheat was differentiated and structured by country or region and cultivar type (spring or winter). Each elemental genome (in particular, A and D) contributed to the structure of the polymorphism studied. We propose that the structure of the wheat germplasm was a result of natural selection under the eco-climatic conditions of cultivation specific to each country or region. As many as 27.4% of cultivars studied violated the requirement of the DUS rules for uniformity, being represented by mixtures of two or more closely related genotypes. However, the composition of a cultivar as a set of related but different genotypes may contribute to its adaptivity, and thereby to the known high plasticity of common wheat.

The genus Musa is one of three genera in the family Musaceae, which includes bananas and plantains, which are monocotyledonous plants. Bananas have valuable nutritional content of vitamin C, B6, minerals, and dietary fiber and are a rich food energy source, given that carbohydrates account for 22%-32% of fruit weight. Molecular markers are valuable for crop improvement and population genetics studies. The availability of whole-genome sequence and in silico approaches has revolutionized bulk marker discovery. We describe an online web genomic resource, BanSatDB (http://webtom.cabgrid.res.in/bansatdb/) having the highest number (>341,000) of putative STR markers from Musa genera so far, represented by three species: M. acuminata (110,000), M. balbisiana (107,000), and M. itinerans (124,000) from 11 chromosomes of each species. BanSatDB has also been populated with 580 validated STR markers from the published literature. It is based on a three-tier architecture using MySQL, PHP and Apache. The markers can be retrieved by use of multiple search parameters including chromosome number(s), microsatellite types (simple or compound), repeat nucleotides (1-6), copy number, microsatellite length, pattern of repeat motif, and chromosome location. These markers can be used for Distinctness, Uniformity and Stability (DUS) tests of variety identification and for marker assisted selection (MAS) in variety improvement and management. These STRs have also proved to be helpful in classification of Musa germplasm to distinguish individual accessions and in the development of a standardized procedure for genotyping. These markers can also be used in gene discovery and QTL mapping. The database represents a source of markers for developing and implementing new approaches for molecular breeding, which are required to enhance banana productivity.

Crop phosphorus (P) deficiency and poor utilization of added P is a major agricultural problem due to reduced solubility of soil P and rapid fixation or precipitation of applied P fertilizer in alkaline and calcareous soils. The effects of P-enriched compost and single superphosphate (SSP) fertilization on maize and wheat yields and P use efficiency in a maize-wheat rotation system were studied for three years. On a three-year average, grain yields of maize and wheat after application of P-enriched compost were increased by 18% and 24%, respectively, in comparison with sole addition of a recommended dose of SSP fertilizer. P-enriched compost addition to soil increased maize and wheat yields by 12% and 17%, respectively, compared to P fertilizer plus FYM incorporation. Soil available P concentration and P uptake were affected significantly by the addition of P-enriched compost. On average, increases in P recovery, use efficiency, and agronomic efficiency of 52%, 18%, and 43% were recorded in maize and increases of 50%, 23%, and 49% in wheat. P-enriched compost application yielded 30% and 32% higher economic returns in maize and wheat than SSP fertilization alone.

Bioactive components are partially responsible for the nutritional and health benefits of soybeans. Four major bioactive components: isoflavones, oligosaccharides, phospholipids, and saponins, were quantified in 763 soybean samples collected from widely distributed regions across China from 2010 to 2013. A majority of the tested bioactive components showed generally declining trends from the north (high latitude) to the south (low latitude). A positive relationship between total oligosaccharides (TO) and altitude was observed. Total isoflavones (TI), phospholipids (TP) and TO were negatively correlated with cumulative temperature above or equal to 15?°C (AT₁₅) and mean daily temperature (MDT), but positively correlated with diurnal temperature range (DTR) and hours of sunshine (HS). Total saponins (TS) were negatively correlated with MDT but positively correlated with rainfall (RF), whereas TO were negatively correlated with RF. Path-coefficient analysis showed that, besides genotype differences, temperature and HS during the reproductive period influenced TI and TP contents, while temperature and RF influenced TS and TO. The effects of weather factors on soybean bioactive components in diverse regions of China were characterized. These findings will be helpful in promoting soybean production for functional food purposes.

The standard cultivation system in the North China Plain is double cropping of winter wheat and summer maize. The main effects of this cultivation system on root development and yield are decreases in soil nutrient content and depth of the plow layer under either long-term no-tillage or rotary tillage before winter wheat sowing and no tillage before summer maize sowing. In this study, we investigated the combined effects of tillage practices before winter wheat and summer maize sowing on soil properties and root growth and distribution in summer maize. Zhengdan 958 (ZD958) was used as experimental material, with three tillage treatments: rotary tillage before winter wheat sowing and no tillage before summer maize sowing (RTW?+?NTM), moldboard plowing before winter wheat sowing and no tillage before summer maize sowing (MPW?+?NTM), and moldboard plowing before winter wheat sowing and rotary tillage before summer maize sowing (MPW?+?RTM). Tillage practice showed a significant (P?<?0.05) effect on grain yield of summer maize. Grain yields under MPW?+?RTM and MPW?+?NTM were 30.6% and 24.0% higher, respectively, than that under RTW?+?NTM. Soil bulk density and soil penetration resistance decreased among tillage systems in the order RTW?+?NTM?>?MPW?+?NTM?>?MPW?+?RTM. Soil bulk densities were 3.3% and 515% lower in MPW?+?NTM and MPW?+?RTM, respectively, than that in RTW?+?NTM, and soil penetration resistances were respectively 17.8% and 20.4% lower, across growth stages and soil depths. Root dry matter and root length density were highest under MPW?+?RTM, with the resulting increased root activity leading to a yield increase of summer maize. Thus the marked effects of moldboard plowing before winter-wheat sowing on root length density, soil penetration resistance, and soil bulk density may contribute to higher yield.