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Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi, threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%-18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and markerassisted selection in maize breeding programs. [ABSTRACT FROM AUTHOR]

Maize is rapidly replacing traditionally cultivated dual purpose crops of South Asia, primarily due to the better economic remuneration. This has created an impetus for improving maize for both grain productivity and stover traits. Molecular techniques can largely assist breeders in determining approaches for effectively integrating stover trait improvement in their existing breeding pipeline. In the current study we identified a suite of potential genomic regions associated to the two major stover quality traits—in-vitro organic matter digestibility (IVOMD) and metabolizable energy (ME) through genome wide association study. However, considering the fact that the loci identified for these complex traits all had smaller effects and accounted only a small portion of phenotypic variation, the effectiveness of following a genomic selection approach for these traits was evaluated. The testing set consists of breeding lines recently developed within the program and the training set consists of a panel of lines from the working germplasm comprising the founder lines of the newly developed breeding lines and also an unrelated diversity set. The prediction accuracy as determined by the Pearson's correlation coefficient between observed and predicted values of these breeding lines were high even at lower marker density (200 random SNPs), when the training and testing set were related. However, the accuracies were dismal, when there was no relationship between the training and the testing set. [ABSTRACT FROM AUTHOR]

Northern Corn Leaf Blight (NCLB) caused by Setosphaeria turcica, is one of the most important diseases of maize world-wide, and one of the major reasons behind yield losses in maize crop in Asia. In the present investigation, a high-resolution genome wide association study (GWAS) was conducted for NCLB resistance in three association mapping panels, predominantly consisting of tropical lines adapted to different agro-ecologies. These panels were phenotyped for disease severity across three locations with high disease prevalence in India. High density SNPs from Genotyping-by-sequencing were used in GWAS, after controlling for population structure and kinship matrices, based on single locus mixed linear model (MLM). Twenty-two SNPs were identified, that revealed a significant association with NCLB in the three mapping panels. Haplotype regression analysis revealed association of 17 significant haplotypes at FDR ≤ 0.05, with two common haplotypes across three maize panels. Several of the significantly associated SNPs/haplotypes were found to be co-located in chromosomal bins previously reported for major genes like Ht2, Ht3 and Htn1 and QTL for NCLB resistance and multiple foliar disease resistance. Phenotypic variance explained by these significant SNPs/haplotypes ranged from low to moderate, suggesting a breeding strategy of combining multiple resistance alleles towards resistance for NCLB. [ABSTRACT FROM AUTHOR]

Key message: Msv1 , the major QTL for MSV resistance was delimited to an interval of 0.87 cM on chromosome 1 at 87 Mb and production markers with high prediction accuracy were developed. Abstract: Maize streak virus (MSV) disease is a devastating disease in the Sub-Saharan Africa (SSA), which causes significant yield loss in maize. Resistance to MSV has previously been mapped to a major QTL ( Msv1) on chromosome 1 that is germplasm and environment independent and to several minor loci elsewhere in the genome. In this study, Msv1 was fine-mapped through QTL isogenic recombinant strategy using a large F population of CML206 × CML312 to an interval of 0.87 cM on chromosome 1. Genome-wide association study was conducted in the DTMA (Drought Tolerant Maize for Africa)-Association mapping panel with 278 tropical/sub-tropical breeding lines from CIMMYT using the high-density genotyping-by-sequencing (GBS) markers. This study identified 19 SNPs in the region between 82 and 93 Mb on chromosome 1(B73 RefGen_V2) at a P < 1.00E-04, which coincided with the fine-mapped region of Msv1. Haplotype trend regression identified a haplotype block significantly associated with response to MSV. Three SNPs in this haplotype block at 87 Mb on chromosome 1 had an accuracy of 0.94 in predicting the disease reaction in a collection of breeding lines with known responses to MSV infection. In two biparental populations, selection for resistant Msv1 haplotype demonstrated a reduction of 1.03-1.39 units on a rating scale of 1-5, compared to the susceptible haplotype. High-throughput KASP assays have been developed for these three SNPs to enable routine marker screening in the breeding pipeline for MSV resistance. [ABSTRACT FROM AUTHOR]

The International Maize and Wheat Improvement Center (CIMMYT), in partnership with several public and private institutions, is working to develop and deploy improved maize (Zea mays L.) germplasm that is drought tolerant, nitrogen use efficient (NUE), and disease resistant for sub-Saharan Africa (SSA), using conventional pedigree selection and molecular breeding. Here, we provide an overview of the progress made on (i) quantitative trait loci (QTL) analysis for drought, NUE, and maize lethal necrosis (MLN); (ii) development of production markers for maize streak virus (MSV) and MLN resistance; and (iii) marker-assisted recurrent selection (MARS) and genomic selection (GS) for developing drought tolerant maize germplasm. We identified several small to moderate effect QTL associated with grain yield and anthesis-silking interval under low N, managed drought, and optimum environments, but only a few small to moderate effect QTL were detected in multiple genetic backgrounds. Thus, CIMMYT is conducting the largest public MARS and GS projects in SSA. A recent comparative study of pedigree selection, MARS and GS undertaken across 8 to 10 bi-parental populations, demonstrated the superior performance of both MARS and GS schemes over pedigree selection. More than 90% of current commercial maize germplasm was found to be highly susceptible to MLN disease. Preliminary mapping studies identified three major QTL for MLN disease resistance, and two are being used for pilot line conversion using marker-assisted backcrossing (MABC). For MSV, pilot marker-assisted selection is ongoing, using three single nucleotide polymorphic (SNP) markers to select a major QTL on chromosome 1. Development of drought tolerant and NUE maize varieties must include MLN resistance in eastern Africa, and we strongly suggest to maize breeders to introgress promising genomic regions for MLN resistance using either conventional or molecular methods. [ABSTRACT FROM AUTHOR]

Identifying quantitative trait loci (QTL) of sizeable effects that are expressed in diverse genetic backgrounds across contrasting water regimes particularly for secondary traits can significantly complement the conventional drought tolerance breeding efforts. We evaluated three tropical maize biparental populations under water-stressed and well-watered regimes for drought-related morpho-physiological traits, such as anthesis-silking interval (ASI), ears per plant (EPP), stay-green (SG) and plant-to-ear height ratio (PEH). In general, drought stress reduced the genetic variance of grain yield (GY), while that of morpho-physiological traits remained stable or even increased under drought conditions. We detected consistent genomic regions across different genetic backgrounds that could be target regions for marker-assisted introgression for drought tolerance in maize. A total of 203 QTL for ASI, EPP, SG and PEH were identified under both the water regimes. Meta-QTL analysis across the three populations identified six constitutive genomic regions with a minimum of two overlapping traits. Clusters of QTL were observed on chromosomes 1.06, 3.06, 4.09, 5.05, 7.03 and 10.04/06. Interestingly, a ~8-Mb region delimited in 3.06 harboured QTL for most of the morpho-physiological traits considered in the current study. This region contained two important candidate genes viz., zmm16 (MADS-domain transcription factor) and psbs1 (photosystem II unit) that are responsible for reproductive organ development and photosynthate accumulation, respectively. The genomic regions identified in this study partially explained the association of secondary traits with GY. Flanking single nucleotide polymorphism markers reported herein may be useful in marker-assisted introgression of drought tolerance in tropical maize. [ABSTRACT FROM AUTHOR]

Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be 'adaptive' to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes. [ABSTRACT FROM AUTHOR]