The objective of this review is to describe events in China and elsewhere that are related to the discovery, genetic identification, use, and ultimate break-down of a single wheat gene for resistance to stripe rust, namely Yr24/Yr26. In our retrospective analysis there was an early assumption of at least three genes at or near the locus, which caused an erroneous presumption of genetic diversity for resistance. It is an example of another boom and bust cycle in plant breeding with races virulent to Yr26 (V26 races) now being the majority race group in the Chinese Pst population. We have attempted to present our story in a historical and personal context demonstrating research inputs from different national and international groups, as well as some significant contemporary side issues. It covers the period from the late 1980s to 2017, during which significant rapid advances in the molecular biology of host: pathogen genetics occurred. We attempt to describe both successes and drawbacks in our work.

With marker and phenotype information from observed populations, genomic selection (GS) can be used to establish associations between markers and phenotypes. It aims to use genome-wide markers to estimate the effects of all loci and thereby predict the genetic values of untested populations, so as to achieve more comprehensive and reliable selection and to accelerate genetic progress in crop breeding. GS models usually face the problem that the number of markers is much higher than the number of phenotypic observations. To overcome this issue and improve prediction accuracy, many models and algorithms, including GBLUP, Bayes, and machine learning have been employed for GS. As hot issues in GS research, the estimation of non-additive genetic effects and the combined analysis of multiple traits or multiple environments are also important for improving the accuracy of prediction. In recent years, crop breeding has taken advantage of the development of GS. The principles and characteristics of current popular GS methods and research progress in these methods for crop improvement are reviewed in this paper.

Genomic selection (GS) as a promising molecular breeding strategy has been widely implemented and evaluated for plant breeding, because it has remarkable superiority in enhancing genetic gain, reducing breeding time and expenditure, and accelerating the breeding process. In this study the factors affecting prediction accuracy (r_MG) in GS were evaluated systematically, using six agronomic traits (plant height, ear height, ear length, ear diameter, grain yield per plant and hundred-kernel weight) evaluated in one natural and two biparental populations. The factors examined included marker density, population size, heritability, statistical model, population relationships and the ratio of population size between the training and testing sets, the last being revealed by resampling individuals in different proportions from a population. Prediction accuracy continuously increased as marker density and population size increased and was positively correlated with heritability; r_MG showed a slight gain when the training set increased to three times as large as the testing set. Low predictive performance between unrelated populations could be attributed to different allele frequencies, and predictive ability and prediction accuracy could be improved by including more related lines in the training population. Among the seven statistical models examined, including ridge regression best linear unbiased prediction (RR-BLUP), genomic BLUP (GBLUP), BayesA, BayesB, BayesC, Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), and reproducing kernel Hilbert space (RKHS), the RKHS and additive-dominance model (Add?+?Dom model) showed credible ability for capturing non-additive effects, particularly for complex traits with low heritability. Empirical evidence generated in this study for GS-relevant factors will help plant breeders to develop GS-assisted breeding strategies for more efficient development of varieties.

In wheat breeding, it is a difficult task to select the most suitable parents for making crosses aimed at the improvement of both grain yield and grain quality. By quantitative genetics theory, the best cross should have high progeny mean and large genetic variance, and ideally yield and quality should be less negatively or positively correlated. Usefulness is built on population mean and genetic variance, which can be used to select the best crosses or populations to achieve the breeding objective. In this study, we first compared five models (RR-BLUP, Bayes A, Bayes B, Bayes ridge regression, and Bayes LASSO) for genomic selection (GS) with respect to prediction of usefulness of a biparental cross and two criteria for parental selection, using simulation. The two parental selection criteria were usefulness and midparent genomic estimated breeding value (GEBV). Marginal differences were observed among GS models. Parental selection with usefulness resulted in higher genetic gain than midparent GEBV. In a population of 57 wheat fixed lines genotyped with 7588 selected markers, usefulness of each biparental cross was calculated to evaluate the cross performance, a key target of breeding programs aimed at developing pure lines. It was observed that progeny mean was a major determinant of usefulness, but the usefulness ratings of quality traits were more influenced by their genetic variances in the progeny population. Near-zero or positive correlations between yield and major quality traits were found in some crosses, although they were negatively correlated in the population of parents. A selection index incorporating yield, extensibility, and maximum resistance was formed as a new trait and its usefulness for selecting the crosses with the best potential to improve yield and quality simultaneously was calculated. It was shown that applying the selection index improved both yield and quality while retaining more genetic variance in the selected progenies than the individual trait selection. It was concluded that combining genomic selection with simulation allows the prediction of cross performance in simulated progenies and thereby identifies candidate parents before crosses are made in the field for pure-line breeding programs.

Genes encoding reporter proteins are used as visual marker-assisted tools in genetic transformation as well as plant breeding. In this study, the red fluorescent protein identified in Discosoma sp. coral (DsRed2) was successfully used as a visual marker for cotton genetic engineering. DsRed2 was successfully expressed in two cotton cultivars, JIN668 and YZ1, driven by the CaMV-35S promoter via the Agrobacterium-mediated transformation. Our results suggest that DsRed2 expression provides an early-stage selection tool for the transgenic calli via visual observation. Red fluorescence can be detected not only in callus and somatic embryos but also in most tissues and organs of mature plants. The transgenic line Yz-2-DsRed2 was crossed with four different cotton cultivars to assess the transgene heritability and stability in different genetic backgrounds. The heritability of the red color was highly stable when Yz-2-DsRed2 was used as a male parent. The DsRed2 gene expressed 100% in the F₁ hybrids. To investigate the relationship between DsRed2 transcription and DNA methylation, a methylation-specific PCR approach was applied to the CaMV-35S promoter region. The results showed a negative association between DNA methylation level in the promoter region and the transgene transcription. Taken together, these findings suggest DsRed2 a visual reporter gene for cotton genetic transformation and molecular breeding programs.

A set of 132 accessions of common millet, Panicum miliaceum L., from 12 provinces of China were assessed for endosperm starch type (waxy or non-waxy) using I₂-KI staining, amylose and amylopectin contents using the dual-wavelength colorimetric method, and genotype of Waxy genes conditioning amylose content by gene sequencing. Endosperm starch content varied from 57.69% to 74.70%, while the amylose and amylopectin contents of the starch ranged from 0 to 23.29% and from 41.99% to 70.24%, respectively. Sequencing two Wx genes, including Wx-L (intron 5-exon 7 and intron 8-9) and Wx-S (exon 9-intron 10) revealed several polymorphisms (S₀, S₋₁₅, L_C, L_F, L_Y). Marker M5-R11 linking to the Wx-S gene may be used to discriminate waxy common millet accessions from non-waxy ones. Among the 132 accessions, 68 with the S₋₁₅ allele had waxy endosperm starch with the amylose content range 0-2.58% and 64 accessions with the S₀ allele had non-waxy endosperm starch with amylose content range 3.94%-23.29%. Five genotypes including S₋₁₅/L_F (45% of the accessions), S₀/L_F (25%), S₀/L_Y (12%), S₀/L_C (11%), and S₋₁₅/L_Y (7%) were identified. Six new SNPs were detected at the Wx-L locus. These results will facilitate common millet breeding, especially of cultivars free of amylose.

Selenium (Se) deficiency commonly occurs in soils of northeastern China and leads to insufficient Se intake by humans. A two-year field study of Se biofortification of common buckwheat supplied with 40?g?Se?ha⁻¹ as selenite (Se(IV)), selenate (Se(VI)), or a combination (1/2 Se(IV?+?VI)) was performed to investigate Se accumulation and translocation in plants and determine the effects of different forms of Se on the grain yield, biomass production, and Se use efficiency of plants and seeds. Se application increased seed Se concentrations to 47.1-265.1?μg?kg⁻¹. Seed Se concentrations following Se(VI) or 1/2 Se(IV?+?VI) treatment exceeded 100?μg?kg⁻¹, an amount suitable for crop Se biofortification. Se concentration in shoots and roots decreased with plant development, and Se translocation from root to shoot in Se(IV)-treated plants was lower than that in plants treated with 1/2 Se(IV?+?VI) and Se(VI). Both grain yield and biomass production increased under 1/2 Se(IV?+?VI) treatment, with grain yields reaching 1663.8 and 1558.5?kg?ha⁻¹ in 2015 and 2016, respectively, reflecting increases of 11.0% and 10.3% over those without Se application. The Se use efficiency of seeds and plants under Se(VI) treatment was significantly higher than those under 1/2 Se(IV?+?VI) and Se(IV) treatments. Thus, application of selenate could result in higher Se accumulation in buckwheat seeds than application of the other Se sources, but the combined application of selenate and selenite might be an alternative approach for improving buckwheat grain yield by Se biofortification in northeastern China.

Barley yellow dwarf virus (BYDV) can infect wheat (Triticum aestivum L.), leading to yield loss. Among four BYDV strains (GAV, GPV, PAV, and RMV) identified in China, BYDV-GAV is the prevailing isolate. YW642, a wheat-Thinopyrum intermedium translocation line, is resistant to BYDV isolates at both seedling and adult stages. Zhong 8601 is the wheat recurrent parent of YW642 and is susceptible to BYDV. In this study, we investigated the adult-stage resistance mechanism of YW642, measured BYDV titer and hydrogen peroxide (H₂O₂) in adult-stage leaves of YW642 and Zhong 8601 inoculated with BYDV-GAV, and identified transcriptional differences between YW642 and Zhong 8601 using microarray-based comparative transcriptomics. Enzyme-linked immunosorbent assay and H₂O₂ assay showed that both BYDV titer and H₂O₂ content were markedly lower in YW642 than in Zhong 8601 at 21, 28, 35, and 40 days post-inoculation (dpi). The transcriptomic comparison revealed that many types of genes were significantly up-regulated at 35 dpi in adult-stage leaves of YW642 compared to Zhong 8601. The important up-regulated genes associated with the adult-stage resistance encoded 15 resistance-like proteins, pathogenesis-related proteins (such as defensin and lipid transfer proteins), protein kinase homologs, transcription factors, reactive oxygen species scavenging-related proteins, and jasmonic acid and gibberellic acid biosynthesis enzymes. These results suggest that precise expression regulation of these proteins plays a crucial role in adult-stage resistance of YW642 against BYDV infection.

Zero-tillage has become increasingly attractive in rice production in China. This study was conducted to determine the feasibility of two possible improved N management practices with fewer N applications in zero-tillage rice: (1) two split applications of urea at 75 kg N ha⁻¹ at mid-tillering and 45 kg N ha⁻¹ at panicle initiation (U_120-2), and (2) a single application of cross-linked polyacrylamide-coated urea (a slow-release fertilizer) at mid-tillering at a rate of 150 kg N ha⁻¹ (PCU_150-1). Three field experiments were conducted to compare grain yield and N-use efficiency among several N treatments: a zero-N control (CK), U_120-2, PCU_150-1, a single application of urea at mid-tillering at a rate of 150 kg N ha⁻¹ (U_150-1), and a commonly recommended N management practice for conventional tillage rice (three split applications of urea with 75 kg N ha⁻¹ as basal, 30 kg N ha⁻¹ at mid-tillering, and 45 kg N ha⁻¹ at panicle initiation) (U_150-3). Treatments with N application (U_120-2, PCU_150-1, U_150-1, and U_150-3) produced 1.08-3.16 t ha⁻¹ higher grain yields than CK. Grain yields under both U_120-2 and PCU_150-1 were comparable to that in U_150-3. Recovery efficiency of N (RE_N), agronomic N-use efficiency (AE_N) and partial factor productivity of applied N (PFP_N) were increased under U_120-2 and were similar under PCU_150-1 to those under U_150-3. U_150-1 showed lower grain yield, RE_N, AE_N, and PFP_N than U_150-3. These results suggest that U_150-3 can be replaced with U_120-2 to achieve both an increase in N-use efficiency and a reduction in number of N applications and or by PCU_150-1 to achieve a maximum reduction in number of N applications in zero-tillage rice production in China.

The content of wheat flour proteins affects the quality of wheat flour. Sulfur nutrition in wheat can change the protein content of the flour. The inconsistency and instability of wheat grain quality during grain filling under high temperature stress (HTS) are a major challenge to the production of high-quality wheat. The effects of sulfur fertilization and HTS on wheat flour protein and its components are unknown. In this study, treatments varying two factors: sulfur fertilization and exposure to short-term HTS, at 20 days post-anthesis, were applied to two wheat cultivars with differing gluten types. Plants of a strong-gluten wheat (Gaoyou 2018) and a medium-gluten wheat (Zhongmai 8) were grown in pots in Beijing in 2015-2017. HTS significantly increased the contents of total protein, albumin, gliadin, glutenin, Cys, and Met in wheat kernels, but reduced grain yield, grain weight, protein yield, globulin content, and total starch accumulation. The HTS-induced increase in total protein amount was closely associated with nitrate reductase (NR) and glutamine synthetase (GS) activities in flag leaves. Sulfur fertilization increased grain and protein yields; grain weight; total protein, albumin, gliadin, glutenin, and globulin contents; protein yield; total starch; Cys, Met; and NR and GS activities. HTS and sulfur fertilization had larger effects on the strong- than on the medium-gluten cultivar. Sulfur fertilization also alleviated the negative effects of HTS on grain yield, protein yield, and starch content. Thus, growing wheat with additional soil sulfur can improve the quality of the flour.

Faba bean (Vicia faba L.) has been identified as a rich source of l-DOPA, which is used in treating Parkinson's disease. Biosynthesis and accumulation of active substances such as l-DOPA in plant tissues may interact with growing conditions and processing methods. Accumulation trends of l-DOPA in various faba bean organs and the effect of drought stress and N fertilization on l-DOPA content were studied in a field and two greenhouse experiments. The influence of various processing methods on l-DOPA content of faba bean tissues was evaluated. The highest l-DOPA content was detected in fresh leaves (22.4?mg?g⁻¹) followed by flowers, young pods, mature seeds, and roots. Regardless of processing method, l-DOPA concentration in faba bean tissues was significantly reduced when tissues were boiled or dried. Among various methods of processing, freezing had the lowest detrimental effect, reducing l-DOPA concentrations by 24.1% and 21.1% in leaves and seeds, respectively. Drought stress elevated l-DOPA concentration, and maximum l-DOPA (23.3?mg?g⁻¹ of biomass) was extracted from plants grown under severe drought stress. However, l-DOPA yield (l-DOPA concentration?×?biomass) was compromised, owing to the adverse influence of drought stress on dry matter production. No significant difference in l-DOPA concentration was detected among various N application rates.

Grass pea (Lathyrus sativus L.) is a crop that is considered one of the more resilient to climate change. With protein-rich seeds and leaves, it has strong potential as human food as well as animal feed and fodder. However, genetic improvement in this crop remains stagnant owing to the poor characterization of its genetic resources. In this study, we characterized 118 accessions of grass pea with 18 EST-SSR markers. A total of 118 accessions, 101 of L. sativus (100 cultivated accessions from Bangladesh and one wild accession) and 17 wild accessions of other Lathyrus species, were used. A total of 67 alleles were detected, with an average of 3.72 alleles per locus and average polymorphism information content of 0.52. A dissimilarity matrix was formed and hierarchical cluster analysis performed using the UPGMA method grouped genotypes into four main clusters. Cluster analysis based on the genetic dissimilarity revealed a clear grouping of the 100 cultivated and 18 wild accessions into four main groups. Group I consisted of 20 accessions with high β-N-oxalyl-l-α,β-diaminopropionic acid (β-ODAP) concentration. Of these 20 accessions, 17 were wild accessions. Only one wild accession (L. cicera) was clustered in group II, which contained 35 accessions. Most of the group II accessions contained low β-ODAP. Group III was represented by 34 accessions, many of them with high β-ODAP. Group IV consisted of 29 accessions, a few of which had very high β-ODAP concentrations. Analysis of molecular variance of the microsatellite data showed significantly higher values of molecular variance between (83%) than within (17%) populations. These characterized accessions will be useful in grass pea breeding programs.