Genetic basis of maize maternal haploid induction beyond MATRILINEAL and ZmDMP.

In maize, doubled haploid (DH) lines are created in vivo through crosses with maternal haploid inducers. Their induction ability, usually expressed as haploid induction rate (HIR), is known to be under polygenic control. Although two major genes (MTL and ZmDMP) affecting this trait were recently described, many others remain unknown. To identify them, we designed and performed a SNP based (~9007) genome-wide association study using a large and diverse panel of 159 maternal haploid inducers. Our analyses identified a major gene near MTL, which is present in all inducers and necessary to disrupt haploid induction. We also found a significant quantitative trait loci (QTL) on chromosome 10 using a case-control mapping approach, in which 793 noninducers were used as controls. This QTL harbors a kokopelli ortholog, whose role in maternal haploid induction was recently described in Arabidopsis. QTL with smaller effects were identified on six of the ten maize chromosomes, confirming the polygenic nature of this trait. These QTL could be incorporated into inducer breeding programs through marker-assisted selection approaches. Further improving HIR is important to reduce the cost of DH line production.

Deciphering the major metabolic pathways associated with aluminum tolerance in popcorn roots using label-free quantitative proteomics.

MAIN CONCLUSION: Al responsive proteins are associated with starch, sucrose, and other carbohydrate metabolic pathways. Sucrose synthase is a candidate to Al tolerance. Al responses are regulated at transcriptional and post-transcriptional levels. Aluminum toxicity is one of the important abiotic stresses that affects worldwide crop production. The soluble form of aluminum (Al3+) inhibits root growth by altering water and nutrient uptake, a process that also reduces plant growth and development. Under long-term Al3+ exposure, plants can activate several tolerance mechanisms. To date, no reports of large-scale proteomic data concerning maize responses to this ion have been published. To investigate the post-transcriptional regulation in response to Al toxicity, we performed label-free quantitative proteomics for comparative analysis of two Al-contrasting popcorn inbred lines and an Al-tolerant commercial hybrid during 72 h under Al-stress conditions. A total of 489 differentially accumulated proteins (DAPs) were identified in the Al-sensitive inbred line, 491 in the Al-tolerant inbred line, and 277 in the commercial hybrid. Among them, 120 DAPs were co-expressed in both Al tolerant genotypes. Bioinformatics analysis indicated that starch, sucrose, and other components of carbohydrate metabolism and glycolysis/gluconeogenesis are the biochemical processes regulated in response to Al toxicity. Sucrose synthase accumulation and an increase in sucrose content and starch degradation suggest that these components may enhance popcorn tolerance to Al stress. The accumulation of citrate synthase suggests a key role for this enzyme in the detoxification process in the Al-tolerant inbred line. The integration of transcriptomic and proteomic data indicates that the Al tolerance response presents a complex regulatory network into the transcription and translation dynamics of popcorn root development.

Major locus for spontaneous haploid genome doubling detected by a case-control GWAS in exotic maize germplasm.

KEY MESSAGE: A major locus for spontaneous haploid genome doubling was detected by a case-control GWAS in an exotic maize germplasm. The combination of double haploid breeding method with this locus leads to segregation distortion on genomic regions of chromosome five. Temperate maize (Zea mays L.) breeding programs often rely on limited genetic diversity, which can be expanded by incorporating exotic germplasm. The aims of this study were to perform characterization of inbred lines derived from the tropical BS39 population using different breeding methods, to identify genomic regions showing segregation distortion in lines derived by the DH process using spontaneous haploid genome doubling (SHGD), and use case-control association mapping to identify loci controlling SHGD. Four different sets were used: BS39_DH and BS39_SSD were derived from the BS39 population by DH and single-seed descendent (SSD) methods, and BS39 × A427_DH and BS39 × A427_SSD from the cross between BS39 and A427. A total of 663 inbred lines were genotyped. The analyses of gene diversity and genetic differentiation for the DH sets provided evidence of the presence of a SHGD locus near the centromere of chromosome 5. The case-control GWAS for the DH set also pinpointed this locus. Haplotype sharing analysis showed almost 100% exclusive contribution of the A427 genome in the same region on chromosome 5 of BS39 × A427_DH, presumably due to an allele in this region affecting SHGD. This locus enables DH line production in exotic populations without colchicine or other artificial haploid genome doubling.

Genomic prediction of maternal haploid induction rate in maize.

Genomic prediction (GP) might be an efficient way to improve haploid induction rate (HIR) and to reduce the laborious and time-consuming task of phenotypic selection for HIR in maize (Zea mays L.). In this study, we evaluated GP accuracies for HIR and other agronomic traits of importance to inducers by independent and cross-validation. We propose the use of GP for cross prediction and parental selection in the development of new inducer breeding populations. A panel of 159 inducers from Iowa State University (ISU set) was genotyped and phenotyped for HIR and several agronomic traits. The data of an independent set of 53 inducers evaluated by the University of Hohenheim (UOH set) was used for independent validation. The HIR ranged from 0.61 to 20.74% and exhibited high heritability (0.90). High cross-validation prediction accuracy was observed for HIR (r = 0.82), whereas for other traits it ranged from 0.36 (self-induction rate) to 0.74 (days to anthesis). Prediction accuracies across different sets were higher when the larger panel (ISU set) was used as a training population (r = 0.54). The average HIR of the 12,561 superior predicted progenies (µSP ) ranged from 1.00-18.36% and was closely related to the corresponding midparent genomic estimated breeding value (GEBV). A predicted genetic variance (VG ) of reduced magnitude was observed in the twenty crosses with highest midparent GEBV or µSP for HIR. Our results indicate that although GP is a useful tool for parental selection, decisions about which cross combinations should be pursued need to be based on optimal trade-offs between maximizing both µSP and VG .