Diverse genetic mechanisms underlie worldwide convergent rice feralization

Background: Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests paddies worldwide and aggressively outcompetes cultivated varieties. Despite increasing attention in recent years, a comprehensive understanding of the origins of weedy crop relatives and how a universal feralization process acts at the genomic and molecular level to allow the rapid adaptation to weediness are still yet to be explored. Results: We use whole-genome sequencing to examine the origin and adaptation of 524 global weedy rice samples representing all major regions of rice cultivation. Weed populations have evolved multiple times from cultivated rice, and a strikingly high proportion of contemporary Asian weed strains can be traced to a few Green Revolution cultivars that were widely grown in the late twentieth century. Latin American weedy rice stands out in having originated through extensive hybridization. Selection scans indicate that most genomic regions underlying weedy adaptations do not overlap with domestication targets of selection, suggesting that feralization occurs largely through changes at loci unrelated to domestication. Conclusions: This is the first investigation to provide detailed genomic characterizations of weedy rice on a global scale, and the results reveal diverse genetic mechanisms underlying worldwide convergent rice feralization

The role of Guanxi in green supply chain management in Asia's emerging economies: A conceptual framework

In recent decades, rapid industrial modernization and economic growth have brought substantial environmental problems such as air pollution, hazardous waste, and water pollution for the Asian Emerging Economies (AEE), in particular China, Taiwan, India, Malaysia, Indonesia, Thailand, and South Korea. These countries have started to adopt green supply chain management (GSCM) as a strategy to reduce the environmental impact. There are anecdotal evidences that the adoption of GSCM in this region is partly influenced by Guanxi – a cultural norm, which plays a significant role in relationship governance within supply chain activities among the AEE. Based on a systematic literature review, we develop a conceptual framework that characterizes the drivers and barriers for the adoption of GSCM practices, incorporating Guanxi as a moderator in the manufacturing sector of the AEE. The conceptual framework addresses the roles of two types of Guanxi in the adoption of GSCM: the relational Guanxi at individual level based on social exchange theory and the aggregated Guanxi at firm level derived from social capital theory. This recognition of Guanxi at two separate decision levels help companies better manage their relationships while they green their supply chains. Directions for future research and managerial implications are discussed accordingly

Ascochyta blight resistance in lentils: Genetics and supporting techniques for breeding

To promote breeding for Ascochyta blight in lentil, the genetics of resistance to lentil Ascochyta blight was investigated. In addition, some techniques needed to support the genetic research and breeding were developed in this study. An efficient procedure for producing genetically true-type plantlets was established based on stimulating elongation of the axilary buds. This technique was then used to multiply F₁ hybrid populations to make the population sizes of different generations large enough for careful genetic analyses. Two regeneration systems, one based on multiple shoot induction from intact seedlings and the other based on cotyledonary node culture, were developed to facilitate the transfer of useful genes from wild lentils and/or other sources into cultivated lentil using tissue culture and genetic engineering techniques. Ten major genes were identified for foliar resistance. The inheritance models for these genes were: one dominant gene for high resistance and one dominant gene for moderate resistance (ILL 5588); a single dominant gene (ILL 5684 and W6 3241), two complementary dominant genes (W3 3192 and Titore), two recessive genes with additive effect (Indian head); one recessive gene (Laird); and one partial dominant gene with large effect and one dominant gene with less effect (W3 3261). The gene in ILL 5684 is allelic to the one in ILL 5588 for high resistance. The contributions of minor genes to Ascochyta blight resistance were established for the first time by creating recombinant inbreds with the same major genotypes but different minor genotypes from two crosses (ILL 5684 x Titore, W6 3241x Titore). A mixed model based analysis carried out for the cross ILL 5588 x Titore indicated that about 30% of the phenotypic variations in segregating populations were due to the minor genes. The overall genetic effect and the partition of the genetic effect into additive, dominant and epistatic effects were done for four crosses using generation-mean analysis. The underlying genetic mechanisms for seed infection rate were more complicated than that for foliar disease severity. The six basic generations were sufficient to model foliar disease severity, whereas they were not sufficient for seed infection rate in two crosses. Dominance played an important role in all crosses for both seed and foliar resistance. Except for foliar resistance in the cross ILL 5684 x Titore, at least one type of inter-gene effect (epstastic) contributed to the increased/reduced resistance. Therefore, selection for resistance would be more efficient if the dominance and epistasis effects were reduced after a few generations of selfing. The major gene for foliar resistance in ILL 5684 is linked to the genes for seed yield/plant or it has pleiotropic effect on seed yield/plant. The gene is independent of the genes for plant height and days to flowering. Within each set, there were significant differences among inbreds for all the three traits. The estimates of heritability based on inbred means were high for seed yield/plant and days to flowering, and moderate for plant height. For the set with major resistance gene, 1) disease severity was not correlated with seed yield/plant and plant height, but weakly and negatively correlated to days to flowering when measured under disease pressure. 2) Seed yield/plant was strongly and positively correlated with plant height, moderately and negatively correlated with days to flowering, and plant height was weakly and positively correlated with days to flowering under both testing conditions. 3) Inbred x environment interaction was not important and selection can be done with or without artificial inoculation. Thus, selection within the set of inbreds with the major resistance gene is required and is feasible for the improvements of yield and other traits and for the utilisation of resistance conferred by minor genes. Based on the results from this study and previous studies, a breeding procedure suitable for the current situation was developed. This procedure is based on crossing resistant and high yielding cultivars and multi-location testing. Gene pyramiding, exploring slow blighting and partial resistance, and using genes contained in wild relatives will be the methods of the future. Identification of more sources of resistance genes, good characterisation of the host-pathogen system, and identification of molecular markers tightly linked to resistance genes are suggested to be the key areas for future study

Genetic Dissection of Leaf Senescence in Rice

Leaf senescence, the final stage of leaf development, is a complex and highly regulated process that involves a series of coordinated actions at the cellular, tissue, organ, and organism levels under the control of a highly regulated genetic program. In the last decade, the use of mutants with different levels of leaf senescence phenotypes has led to the cloning and functional characterizations of a few genes, which has greatly improved the understanding of genetic mechanisms underlying leaf senescence. In this review, we summarize the recent achievements in the genetic mechanisms in rice leaf senescence

A Modified Algorithm for the Improvement of Composite Interval Mapping

Composite interval mapping (CIM) is the most commonly used method for mapping quantitative trait loci (QTL) with populations derived from biparental crosses. However, the algorithm implemented in the popular QTL Cartographer software may not completely ensure all its advantageous properties. In addition, different background marker selection methods may give very different mapping results, and the nature of the preferred method is not clear. A modified algorithm called inclusive composite interval mapping (ICIM) is proposed in this article. In ICIM, marker selection is conducted only once through stepwise regression by considering all marker information simultaneously, and the phenotypic values are then adjusted by all markers retained in the regression equation except the two markers flanking the current mapping interval. The adjusted phenotypic values are finally used in interval mapping (IM). The modified algorithm has a simpler form than that used in CIM, but a faster convergence speed. ICIM retains all advantages of CIM over IM and avoids the possible increase of sampling variance and the complicated background marker selection process in CIM. Extensive simulations using two genomes and various genetic models indicated that ICIM has increased detection power, a reduced false detection rate, and less biased estimates of QTL effects

Association Mapping of Ferrous, Zinc, and Aluminum Tolerance at the Seedling Stage in Indica Rice using MAGIC Populations

Excessive amounts of metal are toxic and severely affect plant growth and development. Understanding the genetic control of metal tolerance is crucial to improve rice resistance to Fe, Zn, and Al toxicity. The multi-parent advanced generation inter-cross (MAGIC) populations were genotyped using a 55 K rice SNP array and screened at the seedling stage for Fe, Zn, and Al toxicity using a hydroponics system. Association analysis was conducted by implementing a mixed linear model (MLM) for each of the five MAGIC populations double cross DC1 (founders were SAGC-08, HHZ5-SAL9-Y3-Y1, BP1976B-2-3-7-TB-1-1, PR33282-B-8-1-1-1-1-1), double cross DC2 (founders of double cross were FFZ1, CT 16658-5-2-2SR-2-3-6MP, IR 68, IR 02A127), eight parents population 8way (founders were SAGC-08, HHZ5-SAL9-Y3-Y1, BP1976B-2-3-7-TB-1-1, PR33282-B-8-1-1-1-1-1, FFZ1, CT 16658-5-2-2SR-2-3-6MP, IR 68, IR 02A127), DC12 (DC1+DC2) and rice multi-parent recombinant inbred line population RMPRIL (DC1+DC2+8way). A total of 21, 30, and 21 QTL were identified for Fe, Zn, and Al toxicity tolerance, respectively. For multi tolerance (MT) as Fe, Zn, and Al tolerance-related traits, three genomic regions, MT1.1 (chr.1: 35.4–36.3 Mb), MT1.2 (chr.1: 35.4–36.3 Mb), and MT3.2 (chr.3: 35.4-36.2 Mb) harbored QTL. The chromosomal regions MT2.1 (chr.2: 2.4–2.8 Mb), MT2.2 (chr.2: 24.5–25.8 Mb), MT4 (chr.4: 1.2 Mb Mb), MT8.1 (chr.8: 0.7–0.9 Mb), and MT8.2 (chr.8: 2.2–2.4 Mb) harbored QTL for Fe and Zn tolerance, while MT2.3 (chr.2: 30.5–31.6 Mb), MT3.1 (chr.3: 12.5–12.8 Mb), and MT6 (chr.6: 2.0–3.0 Mb) possessed QTL for Al and Zn tolerance. The chromosomal region MT9.1 (chr.9: 14.2–14.7 Mb) possessed QTL for Fe and Al tolerance. A total of 11 QTL were detected across different MAGIC populations and 12 clustered regions were detected under different metal conditions, suggesting that these genomic regions might constitute valuable regions for further marker-assisted selection (MAS) in breeding programs

Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy

The advent of molecular markers as a tool to aid selection has provided plant breeders with the opportunity to rapidly deliver superior genetic solutions to problems in agricultural production systems. However, a major constraint to the implementation of marker-assisted selection (MAS) in pragmatic breeding programs in the past has been the perceived high relative cost of MAS compared to conventional phenotypic selection. In this paper, computer simulation was used to design a genetically effective and economically efficient marker-assisted breeding strategy aimed at a specific outcome. Under investigation was a strategy involving the integration of both restricted backcrossing and doubled haploid (DH) technology. The point at which molecular markers are applied in a selection strategy can be critical to the effectiveness and cost efficiency of that strategy. The application of molecular markers was considered at three phases in the strategy: allele enrichment in the BC1F1 population, gene selection at the haploid stage and the selection for recurrent parent background of DHs prior to field testing. Overall, incorporating MAS at all three stages was the most effective, in terms of delivering a high frequency of desired outcomes and at combining the selected favourable rust resistance, end use quality and grain yield alleles. However, when costs were included in the model the combination of MAS at the BC1F1 and haploid stage was identified as the optimal strategy. A detailed economic analysis showed that incorporation of marker selection at these two stages not only increased genetic gain over the phenotypic alternative but actually reduced the over all cost by 40%