Genetic mapping and analysis of traits related to improvement of popcorn

Popcorn and dent maize are distinct gene pools and are maintained and utilized as such in maize breeding programs. Popcorn is inferior to dent maize in traits related to crop productivity. Dent maize is a potential source of favorable alleles to improve the productivity of popcorn, but its utility is hindered by dent alleles with negative effects on popping expansion volume (PEV). If the genetic architecture of popping expansion and other important traits is known in dent x popcorn populations, the negative effects of dent germplasm on PEV may be minimized by marker-assisted selection. Use of DNA markers in breeding programs requires that quantitative trait loci (QTL) associated with target traits be identified. QTL for PEV, kernel weight (KW), growing degree units to anthesis (GDU), and plant height were mapped in F2 plants and their F2:3 families in a dent (B104) x popcorn (BP3) population. Seven QTL associated with 82% of the phenotypic variance were detected for PEV on chromosomes 1 (bins 1.05 and 1.07), 2, 3, 5, 8, and 9. The BP3 allele increased PEV at all QTL except on chromosome 8 where the B104 allele increased PEV. QTL for KW were detected on chromosomes 1 (bins 1.03 and 1.05), 6, 7, 8, and 9. The B104 allele increased KW at all QTL. GDU QTL were detected on chromosomes 1, 2, 3, 4, 6, and 8. For plant height, QTL were detected on chromosomes 1, 2, 8, and 9. QTL for GDU and plant height were in regions where QTL affecting flowering time and plant height were detected in previous studies conducted in dent and flint maize populations. In addition, GDU and plant height QTL were also in regions where genes and other genetic factors affecting both traits have been mapped in maize

Phenotypic assessment of genetic gain from selection for improved drought tolerance in semi-tropical maize populations

Most maize production across the globe is rain-fed, and production is set to be negatively impacted as duration and occurrence of droughts increases due to climate change. Development of water-deficit tolerant maize germplasm has been a major focus for most breeding programmes. Here, we sought to assess the genetic gain for grain yield in two maize populations developed for drought tolerance at CIMMYT by evaluating their cycle progeny through hybrid performance. Inbreds derived from different cycles of the Drought Tolerant Population (DTP) and La Posta Sequia (LPS) were mated to a tester (CML550), and resulting hybrids were evaluated under managed water-deficit stress and well-watered conditions. The difference in yield between water-deficit and well-watered treatments was 27% and 36% for the DTP and LPS, respectively. Genetic gain for grain yield across cycles for the two populations was confirmed in the study. Genetic gain was observed for both treatments indicating that selection for water-deficit stress tolerance simultaneously improves grain yield in well-watered conditions. The DTP population had a genetic gain of 0.07 t ha−1 cycle−1, while the LPS had 0.16 t ha−1 cycle−1 under water-deficit conditions. Significant genetic gain was also observed in the well-watered treatments for both populations. Anthesis to silking interval was significantly reduced under water-deficit stress conditions in both populations. Plant and ear height were reduced in the LPS population in both treatments, while no reductions were observed for the trait in the DTP population. Potential water-deficit stress tolerance donor lines with yields comparable to commercial check varieties were identified

Near-infrared spectroscopy to predict provitamin A carotenoids content in maize

Vitamin A deficiency (VAD) is a public health issue worldwide. Provitamin A (PVA) biofortified maize serves as an alternative to help combat VAD. Breeding efforts to develop maize varieties with high PVA carotenoid content combine molecular and phenotypic selection strategies. The phenotypic assessment of carotenoids is currently done using liquid chromatography, a precise but time-and resource-consuming methodology. Using near-infrared spectroscopy (NIRS) could increase the breeding efficiency. This study used ultra-performance liquid chromatography (UPLC) data from 1857 tropical maize genotypes as a training set and NIRS data to do an independent test of a set of 650 genotypes to predict PVA carotenoids using Bayesian and modified partial least square (MPLS) regression models. Both regression methods produced similar prediction accuracies for the total carotenoids (r2 = 0.75), lutein (r2 = 0.55), zeaxanthin (r2 = 0.61), β-carotene (r2 = 0.22) and β-cryptoxanthin (BCX) (r2 = 0.57). These results demonstrate that Bayesian and MPLS regression of BCX on NIRS data can be used to predict BCX content, the current focus on PVA enhancement, and thus offers opportunities for high-throughput phenotyping at a low cost, especially in the early stages of PVA maize breeding pipeline when many genotypes must be screened

Identification and fine mapping of a major QTL (qRtsc8-1) conferring resistance to maize tar spot complex and validation of production markers in breeding lines

Tar spot complex (TSC) is a major foliar disease of maize in many Central and Latin American countries and leads to severe yield loss. To dissect the genetic architecture of TSC resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid population were used for GWAS and selective genotyping analysis, respectively. A total of 115 SNPs in bin 8.03 were detected by GWAS and three QTL in bins 6.05, 6.07, and 8.03 were detected by selective genotyping. The major QTL qRtsc8-1 located in bin 8.03 was detected by both analyses, and it explained 14.97% of the phenotypic variance. To fine map qRtsc8-1, the recombinant-derived progeny test was implemented. Recombinations in each generation were backcrossed, and the backcross progenies were genotyped with Kompetitive Allele Specific PCR (KASP) markers and phenotyped for TSC resistance individually. The significant tests for comparing the TSC resistance between the two classes of progenies with and without resistant alleles were used for fine mapping. In BC5 generation, qRtsc8-1 was fine mapped in an interval of ~ 721 kb flanked by markers of KASP81160138 and KASP81881276. In this interval, the candidate genes GRMZM2G063511 and GRMZM2G073884 were identified, which encode an integral membrane protein-like and a leucine-rich repeat receptor-like protein kinase, respectively. Both genes are involved in maize disease resistance responses. Two production markers KASP81160138 and KASP81160155 were verified in 471 breeding lines. This study provides valuable information for cloning the resistance gene, and it will also facilitate the routine implementation of marker-assisted selection in the breeding pipeline for improving TSC resistance

Genomic prediction of the performance of hybrids and the combining abilities for line by tester trials in maize

The two most important activities in maize breeding are the development of inbred lines with high values of general combining ability (GCA) and specific combining ability (SCA), and the identification of hybrids with high yield potentials. Genomic selection (GS) is a promising genomic tool to perform selection on the untested breeding material based on the genomic estimated breeding values estimated from the genomic prediction (GP). In this study, GP analyses were carried out to estimate the performance of hybrids, GCA, and SCA for grain yield (GY) in three maize line-by-tester trials, where all the material was phenotyped in 10 to 11 multiple-location trials and genotyped with a mid-density molecular marker platform. Results showed that the prediction abilities for the performance of hybrids ranged from 0.59 to 0.81 across all trials in the model including the additive effect of lines and testers. In the model including both additive and non-additive effects, the prediction abilities for the performance of hybrids were improved and ranged from 0.64 to 0.86 across all trials. The prediction abilities of the GCA for GY were low, ranging between − 0.14 and 0.13 across all trials in the model including only inbred lines; the prediction abilities of the GCA for GY were improved and ranged from 0.49 to 0.55 across all trials in the model including both inbred lines and testers, while the prediction abilities of the SCA for GY were negative across all trials. The prediction abilities for GY between testers varied from − 0.66 to 0.82; the performance of hybrids between testers is difficult to predict. GS offers the opportunity to predict the performance of new hybrids and the GCA of new inbred lines based on the molecular marker information, the total breeding cost could be reduced dramatically by phenotyping fewer multiple-location trials

Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses

CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally

Genetic trends in CIMMYT’s tropical maize breeding pipelines

Fostering a culture of continuous improvement through regular monitoring of genetic trends in breeding pipelines is essential to improve efficiency and increase accountability. This is the first global study to estimate genetic trends across the International Maize and Wheat Improvement Center (CIMMYT) tropical maize breeding pipelines in eastern and southern Africa (ESA), South Asia, and Latin America over the past decade. Data from a total of 4152 advanced breeding trials and 34,813 entries, conducted at 1331 locations in 28 countries globally, were used for this study. Genetic trends for grain yield reached up to 138 kg ha−1 yr−1 in ESA, 118 kg ha−1 yr−1 South Asia and 143 kg ha−1 yr−1 in Latin America. Genetic trend was, in part, related to the extent of deployment of new breeding tools in each pipeline, strength of an extensive phenotyping network, and funding stability. Over the past decade, CIMMYT’s breeding pipelines have significantly evolved, incorporating new tools/technologies to increase selection accuracy and intensity, while reducing cycle time. The first pipeline, Eastern Africa Product Profile 1a (EA-PP1a), to implement marker-assisted forward-breeding for resistance to key diseases, coupled with rapid-cycle genomic selection for drought, recorded a genetic trend of 2.46% per year highlighting the potential for deploying new tools/technologies to increase genetic gain

Vitamin A maize

Non-PRIFPRI2; CRP4; HarvestPlusHarvestPlus; A4NHCGIAR Research Program on Agriculture for Nutrition and Health (A4NH

Genetic mapping and analysis of traits related to improvement of popcorn

Popcorn and dent maize are distinct gene pools and are maintained and utilized as such in maize breeding programs. Popcorn is inferior to dent maize in traits related to crop productivity. Dent maize is a potential source of favorable alleles to improve the productivity of popcorn, but its utility is hindered by dent alleles with negative effects on popping expansion volume (PEV). If the genetic architecture of popping expansion and other important traits is known in dent x popcorn populations, the negative effects of dent germplasm on PEV may be minimized by marker-assisted selection. Use of DNA markers in breeding programs requires that quantitative trait loci (QTL) associated with target traits be identified. QTL for PEV, kernel weight (KW), growing degree units to anthesis (GDU), and plant height were mapped in F2 plants and their F2:3 families in a dent (B104) x popcorn (BP3) population. Seven QTL associated with 82% of the phenotypic variance were detected for PEV on chromosomes 1 (bins 1.05 and 1.07), 2, 3, 5, 8, and 9. The BP3 allele increased PEV at all QTL except on chromosome 8 where the B104 allele increased PEV. QTL for KW were detected on chromosomes 1 (bins 1.03 and 1.05), 6, 7, 8, and 9. The B104 allele increased KW at all QTL. GDU QTL were detected on chromosomes 1, 2, 3, 4, 6, and 8. For plant height, QTL were detected on chromosomes 1, 2, 8, and 9. QTL for GDU and plant height were in regions where QTL affecting flowering time and plant height were detected in previous studies conducted in dent and flint maize populations. In addition, GDU and plant height QTL were also in regions where genes and other genetic factors affecting both traits have been mapped in maize.</p