Water Deficit-Responsive QTLs for Cell Wall Degradability and Composition in Maize at Silage Stage

The use of lignocellulosic biomass for animal feed or biorefinery requires the optimization of its degradability. Moreover, biomass crops need to be better adapted to the changing climate and in particular to periods of drought. Although the negative impact of water deficit on biomass yield has often been mentioned, its impact on biomass quality has only been recently reported in a few species. In the present study, we combined the mapping power of a maize recombinant inbred line population with robust near infrared spectroscopy predictive equations to track the response to water deficit of traits associated with biomass quality. The population was cultivated under two contrasted water regimes over 3 consecutive years in the south of France and harvested at silage stage. We showed that cell wall degradability and β-O-4-linked H lignin subunits were increased in response to water deficit, while lignin and p-coumaric acid contents were reduced. A mixed linear model was fitted to map quantitative trait loci (QTLs) for agronomical and cell wall-related traits. These QTLs were categorized as “constitutive” (QTL with an effect whatever the irrigation condition) or “responsive” (QTL involved in the response to water deficit) QTLs. Fifteen clusters of QTLs encompassed more than two third of the 213 constitutive QTLs and 13 clusters encompassed more than 60% of the 149 responsive QTLs. Interestingly, we showed that only half of the responsive QTLs co-localized with constitutive and yield QTLs, suggesting that specific genetic factors support biomass quality response to water deficit. Overall, our results demonstrate that water deficit favors cell wall degradability and that breeding of varieties that reconcile improved drought-tolerance and biomass degradability is possible

QTL for Yield, Earliness, and Cell Wall Quality Traits in Topcross Experiments of the F838 x F286 Early Maize RIL Progeny

QTL for cell wall digestibility related traits were investigated in maize (Zea mays L.) topcross experiments of 240 RILs obtained from the F838 x F286 early maize hybrid. Genotype effects were highly significant for all agronomic and cell wall related traits and much higher than genotype x environment (GE) interaction effects for cell wall digestibility traits. Eight quantitative trait loci (QTL) for dry matter (DM) yield were observed, out of which only one increasing allele originated from F286. Conversely, three QTL out of four with alleles increasing DM content at silage harvest stage originated from the earliest F286 line. Out of four QTL increasing starch content, two QTL, which originated from F838, did not colocalize with silking date QTL or any other investigated traits. Ten QTL were observed for lignin content and between six and nine QTL were observed for each of the three cell wall digestibility investigated traits. QTL located in bins 1.02 (position 76-80 cM), 1.07 (position 228-230 cM), and 8.07 (position 134-142 cM) are likely of priority interest when it comes to improving maize cell wall digestibility. Candidate genes underlying cell wall digestibility QTL were searched for on the basis of in silico investigations and with maize, Arabidopsis, poplar, and eucalyptus genomic information. In most of QTL positions, transcription factors regulating cell wall lignification were shown to be the currently most plausible candidates involved in genetic variation of maize cell wall digestibility

Energy values of registered corn forage hybrids in France over the last 20 years rose in a context of maintained yield increase

The cultivation of corn silage has developed in France since the 1970s to reach 1.5 million of hectares nowadays. Since 1998, a feeding value criterion (namely UFL for “Unité Fourrage Laitière”) has been taken into account to register forage varieties in the French forage maize hybrids catalog in addition to other criteria related to plant agronomical performances such as yield, earliness and lodging resistance. It is frequently stated that the improvement of plant’s agronomic performances would led to a decline in forage energy value. Decline of “Unité Fourrage Laitière” values has been repeatedly reported and the expected increase was not yet visible in 2002. In the present study, a set 47 early and mid-early hybrids commercialized in France between 1958 and 2015 has been cultivated in 3 locations in France. “Unité Fourrage Laitière” values and yield have been estimated in order to shed light on the evolution of feeding value criteria during this period and to conclude on the evolution of “Unité Fourrage Laitière” values since the introduction of this criterion for registration. Results obtained in our study demonstrated a recent rise in “Unité Fourrage Laitière” value in a context of strong yield increase. This increase was not necessarily attributable to high cob proportion in the harvested silage. Breeder’s work since the 2000’s has succeeded to offer hybrids that recover “Unité Fourrage Laitière” values similar to the ones of hybrids from the 1960’s (Royal, 1960, 91 UFL/100 kg DM). We propose to accentuate this effort targeting the enhancement of lignocellulosic cell wall digestibility to breed for future forage maize hybrids

Genetic variation for lignin content and cell wall digestibility in early maize lines derived from ancient landraces

International audienceRemarkable genetic improvement in maize yield, lodging resistance, biotic and abiotic stress tolerance were obtained during the 1955 - 2000 period in Europe. However, a decline in the average cell wall digestibility of maize hybrids has been observed during the 1980 - 2000 period. This trend has now ceased with the breeding of specialized silage varieties. The cell wall degradability of the best current hybrids does not yet equal that of better old types of the 1960s era such as INRA258, mostly because the germplasm currently used in maize breeding corresponds to progenies of resources initially chosen for grain maize breeding. Nearly 110 new lines were thus derived by self-pollination in old or unused landraces and accessions in order to test the interest of this kind of genetic resources in maize breeding for cell wall degradability traits. Based on per se and topcross experiments, several lines representative of different and new germplasm displayed high or medium high cell wall digestibility. F7103 (Argentina-BBC143), F7104 (Argentina-BBC325), F7106 (Gelderland-VC150), F7114 (Zakarpatskaja-Zeltaja-Zubovidnaja), and F7121 (Comptons-Early) are likely among the more romising new resource lines for improvement of cell wall digestibility in elite dent or flint germplasm. These lines covered a large genetic diversity as F7103 and F7104 are mostly lowland tropical, F7106 and F7121 mostly northern flint, F7114 mostly Oh43/Minnesota13 related. Two other lines of medium-high cell wall digestibility, F7101 (St Engrace) and F7112 (Mecklenburger), were shown to be significantly related to lowland tropical germplasm. Several landraces or old varieties also gave lines of low cell wall digestibility such as F7124 (Curaco-de-Velez) or F7126 (Baanbreker), both related to the northern flint group. Average yield of top-crossed lines was nearly 7 t/ha lower than the average value of the three control hybrids and only one hybrid (F7104 x UH002) had yield and earliness equal to those of control hybrids. These low values were related to the fact that investigated lines were derived from old resources that did not get the last 60 years genetic improvements, and also to the only use of a flint male for top-crosses that did not optimize the genetic distance with all top-crossed lines. Allele sequencing and association genetics should give markers for targeted introgression of new alleles of interest originating from this specific set of lines in elite lines

First results from a pyramidal recurrent selection system for breeding maize silage

The pyramidal recurrent selection system which is presented for breeding maize silage is designed to enhance variety development by preparing elite populations. From an early synthetic dent, two synthetics were developed: the 'base' synthetic with a low selection rate and the 'elite' synthetic with a high selection rate. Two cycles of recurrent selection with tester were achieved through this system, using multitrait selection with one-year evaluation of dry matter yield and dry matter content in three locations. The mean of 'elite' synthetic was 2.7 % better than 'base' synthetic for dry-matter yield in the second cycle. Genetic variance of 'elite' synthetic appeared to be about 50 % of that of 'base' population for dry matter yield in cycle 2 and for dry matter content in both cycles. Genotype x environment interaction variance was the same for both types of populations. Thus, strong differences in genetic variances were associated to relatively small differences in means. Results are discussed in terms of the effects of selection intensity, multitrait selection and genetic drift. (© Inra/Elsevier, Paris.)Premiers résultats d'un schéma de sélection pyramidal pour l'amélioration du maïs ensilage. Un schéma de sélection récurrente pyramidale est proposé pour le maïs ensilage afin de favoriser les sorties vers la création variétale. Partant d'une synthétique dentée précoce, deux synthétiques ont été développées : une synthétique de « base » conduite à une faible intensité de sélection et une synthétique « élite » conduite à forte intensité de sélection. Selon ce schéma, deux cycles de sélection récurrente avec testeur ont été réalisés avec, pour chaque cycle, une année d'évaluation dans trois lieux du rendement en matière sèche et de la teneur en matière sèche. Au second cycle, le rendement du niveau élite a été supérieur de 2,7 % à celui du niveau base. La variance génétique du niveau « élite » est apparue nettement plus faible (50 %) que pour le niveau « base » au deuxième cycle pour le rendement et dans les deux cycles pour la teneur en matière sèche. La variance d'interaction génotype x environnement a été la même pour les deux populations. Les résultats sont discutés en termes d'effets de l'intensité de la sélection, de la sélection multicaractère et de la dérive génétique. (© Inra/Elsevier, Paris.

Quantitative trait loci mapping in hybrids between Dent and Flint maize multiparental populations reveals group-specific QTL for silage quality traits with variable pleiotropic effects on yield

International audienceKey messageSilage quality traits of maize hybrids between the Dent and Flint heterotic groups mostly involved QTL specific of each parental group, some of them showing unfavorable pleiotropic effects on yield.AbstractMaize (Zea mays L.) is commonly used as silage for cattle feeding in Northern Europe. In addition to biomass production, improving whole-plant digestibility is a major breeding objective. To identify loci involved in the general (GCA, parental values) and specific combining ability (SCA, cross-specific value) components of hybrid value, we analyzed an incomplete factorial design of 951 hybrids obtained by crossing inbred lines issued from two multiparental connected populations, each specific to one of the heterotic groups used for silage in Europe (Dent and Flint). Inbred lines were genotyped for approximately 20K single nucleotide polymorphisms, and hybrids were phenotyped in eight environments for seven silage quality traits measured by near-infrared spectroscopy, biomass yield and precocity (partly analyzed in a previous study). We estimated variance components for GCA and SCA and their interaction with environment. We performed QTL detection using different models adapted to this hybrid population. Strong family effects and a predominance of GCA components compared to SCA were found for all traits. In total, 230 QTL were detected, with only two showing SCA effects significant at the whole-genome level. More than 80% of GCA QTL were specific of one heterotic group. QTL explained individually less than 5% of the phenotypic variance. QTL co-localizations and correlation between QTL effects of quality and productivity traits suggest at least partial pleiotropic effects. This work opens new prospects for improving maize hybrid performances for both biomass productivity and quality accounting for complementarities between heterotic groups

Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering.

When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred "Flint-Dent" panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species

Genome-wide SNP genotyping of DNA pools identifies original landraces to enrich maize breeding genepools

International audienceMaize landraces germplasm have a very large genetic diversity that is still poorly characterized and exploited in plant breeding programs. We studied the effect of both human selection and environmental adaptation on genome-wide diversity of landraces with a focus on landraces-hybrid transition in order to identify interesting source of genetic diversity to enlarge modern breeding pools. We developed a high-throughput, cheap and labor saving DNA pooling approach based on 50K SNP maize Illumina array and estimated thereby allelic frequencies of 23412 SNP in 156 landraces representing worldwide maize diversity. We compared the diversity of this collection at genome-wide scale level with that of a panel of 336 inbred lines. Our new approach: (i) gives accurate allelic frequencies estimation that are reproducible across laboratories, (ii) protects both against false detection of allele presence within landraces and against ascertainment bias. Modified Roger's genetic Distance estimated from 23412 SNP and 17 SSR on same DNA pool are highly correlated, which validates our approach. Accordingly, structuration analysis based on SNP gives consistent results with SSR for higher levels of structuration but gives a slightly different pictures for more advanced structuration levels, suggesting that SNP and SSR could capture differently recent evolution. Gene diversity of landraces varies strongly along the genome and according to geographic origins. We identified 376 SNP under diversifying selection unraveling a selective footprints in Tga1/Su1 regions. While some maize landraces were closely related to several inbred lines and strongly contributed to modern breeding pools as Reid Yellow Dent or Lancaster Surecrop, some other have no related inbred lines and seem to have poorly contributed. We identified limited diversity loss or selective sweep between landraces and inbred lines, excepted in centromeric regions. For these regions, original landraces could be interesting to enlarge genetic diversity of modern breeding pool

Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array Mariangela Arca

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains however poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on SNP Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 SSRs using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species