Loci and candidate gene identification for soybean resistance to Phytophthora root rot race 1 in combination with association and linkage mapping

Molecular Breeding - Northern corn leaf blight (NCLB) is one of the main diseases of maize, which greatly reduces production and causes millions of dollars in losses worldwide annually....     

A rice GDSL esterase/lipase protein (GELP) is required for anther and pollen development

Molecular Breeding - Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae), is one of the most devastating diseases in maize that not only severely reduces grain...     

Development of a sequence-tagged site (STS) marker for sex identification in the dioecious rattan species Calamus guruba Buch.-Ham.

Molecular Breeding - With the decrease of cost in genotyping, single nucleotide polymorphisms (SNPs) have gained wide acceptance because of their abundance, even distribution throughout the maize...     

Turning Maize Cobs into a Valuable Feedstock

With rising energy demand and limited resources, the need for alternative energy production is increasing. Maize cobs have an advantageous composition for the production of biofuels such as cellulosic ethanol but are currently left unused on the fields after harvest. Furthermore, cobs contain a low concentration of nitrogen (<1%). Therefore, cob harvest will not deplete soil fertility. Consequently, maize cobs are a cheap and promising source for sustainable energy production. Yet with primary focus on grain yield, no or little effort has been spent to increase cob biomass yield in addition to grain yield. Both cob and grain yield are complex inherited traits affected by the environment. Breeding of dual-purpose maize varieties with simultaneously increased cob and grain yield requires a deeper understanding of factors influencing both cob and grain development. In this article, the available knowledge on the genetics of cob formation and current and future applications of maize cob utilization are discussed to evaluate the prospects for development of dual-purpose maize varieties.     

Evaluation of the yield and nitrogen use efficiency of the dominant maize hybrids grown in North and Northeast China

Breeding high-yielding and nutrient-efficient cultivars is one strategy to simultaneously resolve the problems of food security,resource shortage,and environmental pollution.However,the potential increased yield and reduction in fertilizer input achievable by using high-yielding and nutrient-efficient cultivars is unclear.In the present study,we evaluated the yield and nitrogen use efficiency(NUE) of 40 commercial maize hybrids at five locations in North and Northeast China in 2008 and 2009.The effect of interaction between genotype and nitrogen(N) input on maize yield was significant when the yield reduction under low-N treatment was 25%-60%.Based on the average yields achieved with high or low N application,the tested cultivars were classified into four types based on their NUE:efficient-efficient(EE) were efficient under both low and high N inputs,high-N efficient(HNE) under only high N input,low-N efficient(LNE) under only low N input,and nonefficient-nonefficient under neither low nor high N inputs.Under high N application,EE and HNE cultivars could potentially increase maize yield by 8%-10% and reduce N input by 16%-21%.Under low N application,LNE cultivars could potentially increase maize yield by 12%.We concluded that breeding for N-efficient cultivars is a feasible strategy to increase maize yield and/or reduce N input.     

Resistance to Striga hermonthica in a maize inbred line derived from Zea diploperennis

Breeding for resistance to Striga in maize (Zea mays), with paucity of donor source and known mechanisms of resistance, has been challenging. Here, post-attachment development of S. hermonthica was monitored on two maize inbreds selected for field resistance and susceptibility reactions to Striga at the International Institute of Tropical Agriculture. Haustorial invasion of the parasite into roots of these inbreds was examined histologically. Morphological differences were observed between roots of the susceptible and the resistant inbreds. The resistant maize had fewer Striga attachments, delayed parasitic development and higher mortality of attached parasites compared with the susceptible inbred. Striga on the susceptible inbred usually penetrated the xylem and showed substantial internal haustorial development. Haustorial ingress on the resistant inbred was often stopped at the endodermis. Parasites able to reach resistant host xylem vessels showed diminished haustorial development relative to those invading susceptible roots. These results suggest that the resistant inbred expresses a developmental barrier and incompatible response against Striga parasitism.     

In vitro plant regeneration from quality protein maize (QPM)

Breeding efforts to obtain more nutritious maize materials aimed at alleviating dietary deficiencies in developing countries have resulted in an improved maize germplasm known as quality protein maize (QPM). Quality protein maize has higher contents of tryptophan, lysine, and leucine than common maize, but suffers from some major agronomic drawbacks found in common inbred maize lines, such as susceptibility to insect pests and fungal and bacterial diseases and herbicide sensitivity. The development of a reproducible and efficient protocol for tissue culture of QPM is expected to solve some of these deficiencies. In this work, we have evaluated different formulations for in vitro induction of morphogenic responses in three QPM lines developed by the International Maize and Wheat Improvement Center (CIMMYT): CML (CIMMYT maize line)-145, CML-176, and CML-186. Only CML-176 and CML-186 have proven to be responsive to the in vitro conditions considered in this work, with CML-176 showing the highest efficiency in regenerable callus formation and growth. N6C1 medium was found to be efficient for in vitro culture of QPM, whereas no plants could be regenerated by using MPC medium. From CML-176 embyogenic calli cultured on N6C1 medium, we were able to regenerate up to 0.3 plants per 500 mg fresh weight (FW) callus. Further modifications in this experimental protocol, including the replacement of 3,6-dichloro-o-anisic acid with 2,4-dichlorophenoxyacetic acid and modification of the N6C1 vitamin balance, significantly increased the regeneration response of the induced calli, with up to 16.8 and 9.3 plants recovered per 500 mg FW callus for CML-176 and CML-186, respectively.     

Mining of Candidate Maize Genes for Nitrogen Use Efficiency by Integrating Gene Expression and QTL Data

Breeding maize varieties for high nitrogen (N) use efficiency (NUE) by marker-assisted selection using NUE quantitative trait locus (QTL) or by genetic transfer of NUE-associated genes is a viable approach for increasing grain yield in N-limited production areas. In this investigation, we evaluated a set of introgression line populations under N supply and N deficiency conditions. From 42 QTLs for grain yield and yield components, 23 were identified under N supply conditions and 33 from N limited conditions. Meta-analysis of published maize NUE QTLs revealed 37 “consensus” QTLs, of which, 18 was detected under low N conditions. In addition, 258 unique ESTs associated with low N stress response, N uptake, transport, and assimilation were aligned on the maize genome by in silico mapping. Integrating the EST map with the QTL map has resulted in the identification of candidate NUE-associated genes of the following functional categories: N uptake, transport, and assimilation; carbon (C) metabolism and assimilation; and cascades of stress response and signal transduction genes. Nine candidates that have been introgressed into Ye478 significantly altered grain yield/yield components. It is suggested that the dynamics of interactions between C and N metabolism are important for maize yield. A high NUE variety should have a highly efficient C assimilation per unit N and actively express CO₂ assimilation-related genes under N-limited conditions.     

Breeding maize as biogas substrate in Central Europe: II. Quantitative-genetic parameters for inbred lines and correlations with testcross performance

Breeding maize for use as a biogas substrate (biogas maize) has recently gained considerable importance. To optimize hybrid breeding programs, information about line per se performance (LP) of inbreds and its relation to their general combining ability (GCA) is required. The objectives of our research were to (1) estimate variance components and heritability of LP for agronomic and quality traits relevant to biogas production, (2) study correlations among traits as well as between LP and GCA, and (3) discuss implications for breeding of biogas maize. We evaluated 285 diverse dent maize inbred lines in six environments. Data were recorded on agronomic and quality traits, including dry matter yield (DMY), methane fermentation yield (MFY), and their product, methane yield (MY), as the main target trait. In agreement with observations made for GCA in a companion study, variation in MY was mainly determined by DMY. MFY, which showed moderate correlation with lignin but only weak correlation with starch, revealed only low genotypic variation. Thus, our results favor selection of genotypes with high DMY and less focus on ear proportion for biogas maize. Genotypic correlations between LP and GCA [r _g (LP, GCA)] were highest (≥0.94) for maturity traits (days to silking, dry matter concentration) and moderate (≥0.65) for DMY and MY. Multistage selection is recommended. Selection for GCA of maturity traits, plant height, and to some extent also quality traits and DMY on the level of LP looks promising.     

Maize plants infestation by Fusarium spp. and deoxynivalenol in genetically modified corn hybrid and traditional maize cultivars

The objective of the performed investigations was to isolate pathogenic fungi from contaminated maize cobs, to assess the appearance of maize cob fusariosis and to determine grain contamination with deoxynivalenol in the cultivation of genetically modified maize containing a gene resistance against European corn borer (Ostrinia nubilalis Hbn) as well as selected non-modified cultivars. The plant material comprised the following genetically modified maize cultivar: DKC 3421 YG (MON 810) and non-modified cultivars obtained from Smolice Plant Breeding Ltd., IHAR Group: Junak (FAO 210-220), Prosna (FAO 220), SMH (FAO 230), Baca (FAO 220). Prior to harvesting, the occurrence of maize cob fusariosis was determined in the 89 (BBCH) developmental ripening stage. Microbiological assessment was carried out on grains selected from cobs characterized by various pathological symptoms. In 2008, a total of 133 isolates was obtained from the examined samples of infected maize plants, of which 51 isolates were species-identified, while in 2009, the total of 123 isolates were determined, of which 63 were species-identified. In both experimental years, the majority of isolates contained fungi from the Fusarium genus. The performed analysis of mean levels of cob contamination by fusarioses revealed that DKC 3421 YG (MON 810) and SMH (FAO 230) cultivars showed the smallest levels of contamination as well as the lowest percent of cob contamination per plant, while Junak (FAO 210-220) and Baca (FAO 220) cultivars were characterized by the highest degree of contamination. The lowest deoxynivalenol concentrations were determined in years 2008 and 2009 in the case of the DKC 3421 YG (MON 810) cultivar, whereas Prosna (FAO 220) cultivar was characterized by the highest deoxynivalenol concentration.     

Heterochromatic regions in corn A- and B- chromosomes

A collection of maize forms from the Vavilov All-Russia Institute of Plant Breeding (VIR) was studied. We compared variation in the following traits: the number and size of heterochromatic knob regions (HKRs) of chromosomes of mother pollen cells at pachytene depending on the presence (B+) or absence (B0) of B-chromosomes; size of B-chromosomes (general, of heterochromatic part); and the frequency of B+ plants in groups of forms contrasting in the HKR number (10-15, 4-10, 2-7, 1-4). It was shown that B chromosomes had statistically significantly different effects on HKR polymorphism, relative heterochromatin "content" in the cell of multiknob and knobless forms, selection of plants for early ear flowering in these forms. The combination of maximum (and minimum) sizes of heterochromatic regions of A- and B-chromosomes was established; the genomic level of control of the trait is suggested. The role of the relationship of polymorphism at heterochromatic regions of A- and B-chromosomes between them and with the systems of maize reproduction is considered as a mechanism of maintenance of optimum plant heterozygosity via adaptive ontogenetic redistribution of heterochromatin among loci, chromosomes, and gametes.     

Modern maize hybrids in Northeast China exhibit increased yield potential and resource use efficiency despite adverse climate change

The impact of global changes on food security is of serious concern. Breeding novel crop cultivars adaptable to climate change is one potential solution, but this approach requires an understanding of complex adaptive traits for climate‐change conditions. In this study, plant growth, nitrogen (N) uptake, and yield in relation to climatic resource use efficiency of nine representative maize cultivars released between 1973 and 2000 in China were investigated in a 2‐year field experiment under three N applications. The Hybrid‐Maize model was used to simulate maize yield potential in the period from 1973 to 2011. During the past four decades, the total thermal time (growing degree days) increased whereas the total precipitation and sunshine hours decreased. This climate change led to a reduction of maize potential yield by an average of 12.9% across different hybrids. However, the potential yield of individual hybrids increased by 118.5 kg ha^?1 yr^?1 with increasing year of release. From 1973 to 2000, the use efficiency of sunshine hours, thermal time, and precipitation resources increased by 37%, 40%, and 41%, respectively. The late developed hybrids showed less reduction in yield potential in current climate conditions than old cultivars, indicating some adaptation to new conditions. Since the mid‐1990s, however, the yield impact of climate change exhibited little change, and even a slight worsening for new cultivars. Modern breeding increased ear fertility and grain‐filling rate, and delayed leaf senescence without modification in net photosynthetic rate. The trade‐off associated with delayed leaf senescence was decreased grain N concentration rather than increased plant N uptake, therefore N agronomic efficiency increased simultaneously. It is concluded that modern maize hybrids tolerate the climatic changes mainly by constitutively optimizing plant productivity. Maize breeding programs in the future should pay more attention to cope with the limiting climate factors specifically.     

Genome-wide association study for soybean mosaic virus SC3 resistance in soybean

Molecular Breeding - Meloidogyne graminicola is one of the most important plant-parasitic nematodes in rice. Breeding for natural resistance and tolerance is considered one of the most economical...     

Transcriptional and Metabolic Changes Associated to the Infection by Fusarium verticillioides in Maize Inbreds with Contrasting Ear Rot Resistance

Fusarium verticillioides causes ear rot and grain mycotoxins in maize (Zea mays L.), which are harmful to human and animal health. Breeding and growing less susceptible plant genotypes is one alternative to reduce these detrimental effects. A better understanding of the resistance mechanisms would facilitate the implementation of strategic molecular agriculture to breeding of resistant germplasm. Our aim was to identify genes and metabolites that may be related to the Fusarium reaction in a resistant (L4637) and a susceptible (L4674) inbred. Gene expression data were obtained from microarray hybridizations in inoculated and non-inoculated kernels from both inbreds. Fungal inoculation did not produce considerable changes in gene expression and metabolites in L4637. Defense-related genes changed in L4674 kernels, responding specifically to the pathogen infection. These results indicate that L4637 resistance may be mainly due to constitutive defense mechanisms preventing fungal infection. These mechanisms seem to be poorly expressed in L4674; and despite the inoculation activate a defense response; this is not enough to prevent the disease progress in this susceptible line. Through this study, a global view of differential genes expressed and metabolites accumulated during resistance and susceptibility to F. verticillioides inoculation has been obtained, giving additional information about the mechanisms and pathways conferring resistance to this important disease in maize.     

Biochemical and genetic analyses of N metabolism in maize testcross seedlings: 2. Roots

Key message

Intracellular factors differentially affected enzyme activities of N assimilation in the roots of maize testcrosses where alanine aminotransferase and glutamate synthase were the main enzymes regulating the levels of glutamate.

Abstract

N is a key macronutrient for plant growth and development. Breeding maize with improved efficiency in N use could help reduce environmental contamination as well as increase profitability for the farmers. Quantitative trait loci (QTL) mapping of traits related to N metabolism in the root tissue was undertaken in a maize testcross mapping population grown in hydroponic cultures. N concentration was negatively correlated with root and total dry mass. Neither the enzyme activities nor metabolites were appreciably correlated between the root and leaf tissues. Repeatability measures for most of the enzymes were lower than for dry mass. Weak negative correlations between most of the enzymes and dry mass resulted likely from dilution and suggested the presence of excess of enzyme activities for maximal biomass production. Glutamate synthase and alanine aminotransferase each explained more variation in glutamate concentration than either aspartate aminotransferase or asparagine synthetase whereas glutamine synthetase was inconsequential. Twenty-six QTL were identified across all traits. QTL models explained 7–43% of the variance with no significant epistasis between the QTL. Thirteen candidate genes were identified underlying QTL within 1-LOD confidence intervals. All the candidate genes were located in trans configuration, unlinked or even on different chromosomes, relative to the known genomic positions of the corresponding structural genes. Our results have implications in improving NUE in maize and other crop plants.

     

Quantitative Trait Loci Mapping of Maize Yield and Its Components Under Different Water Treatments at Flowering Time

Drought or water stress is a serious agronomic problem resulting in maize (Zea mays L.) yield loss throughout the world. Breeding hybrids with drought tolerance is one important approach for solving this problem. However, lower efficiency and a longer period of breeding hybrids are disadvantages of traditional breeding programs. It is generally recognized that applying molecular marker techniques to traditional breeding programs could improve the efficiency of the breeding of drought‐tolerant maize. To provide useful information for use in studies of maize drought tolerance, the mapping and tagging of quantitative trait loci (QTL) for yield and its components were performed in the present study on the basis of the principle of a mixed linear model. Two hundred and twenty‐one recombinant inbred lines (RIL) of Yuyu 22 were grown under both well‐watered and water‐stressed conditions. In the former treatment group, plants were well irrigated, whereas those in the latter treatment group were stressed at flowering time. Ten plants of each genotype were grown in a row that was 3.00 m × 0.67 m (length × width). The results show that a few of the QTL were the same (one additive QTL for ear length, two additive QTL and one pair of epistatic QTL for kernel number per row, one additive QTL for kernel weight per plant), whereas most of other QTL were different between the two different water treatment groups. It may be that genetic expression differs under the two different water conditions. Furthermore, differences in the additive and epistatic QTL among the traits under water‐stressed conditions indicate that genetic expression also differs from trait to trait. Major and minor QTL were detected for the traits, except for kernel number per row, underwater‐stressed conditions. Thus, the genetic mechanism of drought tolerance in maize is complex because the additive and epistatic QTL exist at the same time and the major and minor QTL all contribute to phenotype under water‐stressed conditions. In particular, epidemic QTL under water‐stressed conditions suggest that it is important to investigate the drought tolerance of maize from a genetic viewpoint. (Managing editor: Wei Wang)     

Anthocyanin accumulation enhanced in <Emphasis Type="Italic">Lc</Emphasis>-transgenic cotton under light and increased resistance to bollworm

Breeding of naturally colored cotton fiber has been hampered by the limited germplasm, an alternative way is to use transgenic approach to create more germplasm for breeding. Here, we report our effort to engineer anthocyanin production in cotton. The maize Lc gene, under the control of the constitutive 35S promoter, was introduced into cotton through genetic transformation. Our data showed that the expression of the Lc gene alone is sufficient to trigger the accumulation of anthocyanin in a variety of cell types including fiber cells in cotton. However, the accumulation of colored anthocyanin in cotton fibers requires the participation of light signaling. These data indicate that it is feasible to engineer colored fibers through transgenic approach in cotton. Furthermore, we showed that the Lc-transgenic cotton plants are resistant to cotton bollworm. These transgenic plants are, therefore, potentially useful for cotton breeding against cotton bollworm.     

Biochemical and genetic analyses of N metabolism in maize testcross seedlings: 1. Leaves

Key message

Aside from the identification of 32 QTL for N metabolism in the seedling leaves of a maize testcross population, alanine aminotransferase was found to be a central enzyme in N assimilation.

Abstract

Excessive application of nitrogen (N) fertilizer to grow commercial crops like maize is a cause of concern because of the runoff of excess N into streams and rivers. Breeding maize with improved N use efficiency (NUE) would reduce environmental pollution as well as input costs for the farmers. An understanding of the genetics underlying N metabolism is key to breeding for NUE. From a set of 176 testcrosses derived from the maize IBMsyn10 population grown in hydroponics, we analyzed the youngest fully expanded leaf at four-leaf stage for enzymes and metabolites related to N metabolism. Three enzymes, along with one metabolite explained 24% of the variation in shoot dry mass. Alanine aminotransferase (AlaAT) stood out as the key enzyme in maintaining the cellular level of glutamate as it alone explained 58% of the variation in this amino acid. Linkage mapping revealed 32 quantitative trait loci (QTL), all trans to the genomic positions of the structural genes for various enzymes of N assimilation. The QTL models for different traits accounted for 7–31% of the genetic variance, whereas epistasis was generally not significant. Five coding regions underlying 1-LOD QTL confidence intervals were identified for further validation studies. Our results provide evidence for the key role of AlaAT in N assimilation likely through homeostatic control of glutamate levels in the leaf cells. The two QTL identified for this enzyme would help to select desirable recombinants for improved N assimilation.

     

SNP markers linked to leaf rust and grain mold resistance in sorghum

Grain mold and rust are diseases that can significantly reduce sorghum grain yield. Breeding for resistance to these diseases is hindered by inefficient disease screening. A viable option to greatly improve breeding efficiency is to identify molecular markers or genes linked to the host resistance. In this study, we applied 14,739 single nucleotide polymorphism markers to the sorghum mini core of 242 accessions that had been evaluated for rust resistance in both greenhouse and field and for grain mold in the field for 2 years. Through association mapping we have identified two loci linked to grain mold resistance and five loci linked to rust resistance. Among the two loci linked to grain mold resistance, one contained a homolog of the maize nonhost resistance gene Rxo1. Two of rust-linked loci each contained the rust resistance gene homologous to the maize rust resistance gene Rp1-D which is the B locus (the A locus containing Pu was not linked in this study) and to the wheat rust resistance gene Lr1. The remaining loci contained genes important in other steps of the defense response, such as cyclophilins that mediate resistance response preceding hypersensitive response (HR) and Hin1 directly involved in producing HR. The results from this study will facilitate marker-assisted selection of host resistance to grain mold and rust in sorghum.     

Potential hosts of Prostephanus truncatus (Coleoptera: Bostrichidae) among native and agroforestry trees in Kenya

This study was carried out to establish the extent to which an invasive stored products pest, Prostephanus truncatus Horn exploits wood as a feeding and breeding resource in Kenya. Twenty seven out of 84 native and agroforestry trees and shrubs supported the breeding of P. truncatus under laboratory conditions. Adult survival (<1% to 18%) for 8 weeks was recorded on 51 tree species that did not support breeding. The breeding success of this beetle varied widely between host tree species and showed no obvious trends based on tree systematics or wood hardness. Studies of P. truncatus survival on two host tree species found that the greatest increase in the P. truncatus population occurred on stem sapwood, whilst the smallest population increase was on twigs. Breeding also varied greatly from season to season; studies on ten selected host species showed that reproduction was often greatest in wood samples collected and tested during the dry season in September. The implications of these findings for the management of P. truncatus infestations in farm stored maize are discussed.