Tropical Lines Research Articles

Registration of provitamin A‐enriched tropical maize inbred lines

AbstractVitamin A deficiency and its associated disorders are pervasive in sub‐Saharan Africa (SSA) including many middle‐ and low‐income countries across the world. Provitamin A‐enriched maize (Zea mays L.) inbred lines with desirable agronomic and adaptive traits have been developed and used to generate and commercialize maize varieties with medium to high levels of provitamin A in a few countries to curb vitamin A deficiency. Nonetheless, these inbred lines have not been made widely available to the public and private sector breeders in many countries. The main purpose for releasing the 21 provitamin A‐enriched tropical maize inbred lines (PI 705424–PI 705444, Reg. nos. GP‐624–GP‐644) is to supply maize breeders with elite source germplasm for increasing provitamin A and other carotenoids to much higher levels to offset losses during storage, natural degradation, and processing. These inbred lines were developed at the International Institute of Tropical Agriculture (IITA) from backcrosses of high β‐carotene temperate lines as donors and elite tropical lines as recipients. These inbred lines were developed through repeated self‐pollination with rigorous visual selection among and within lines for plant vigor, synchronous silk emergence and pollen shedding, low ear placement, and resistance to lodging and major tropical diseases, followed by selection for bright yellow to orange kernel color with semi flint to flint kernel texture after harvest. The released maize inbred lines will be diverse sources of favorable alleles to accelerate genetic gain in provitamin A and other beneficial carotenoid enrichment for human health.

Tropical graph curves

We study tropical line arrangements associated to a three-regular graph $G$ that we refer to as tropical graph curves. Roughly speaking, the tropical graph curve associated to $G$ , whose genus is $g$ , is an arrangement of $2g-2$ lines in tropical projective space that contains $G$ (more precisely, the topological space associated to $G$ ) as a deformation retract. We show the existence of tropical graph curves when the underlying graph is a three-regular, three-vertex-connected planar graph. Our method involves explicitly constructing an arrangement of lines in projective space, i.e. a graph curve whose tropicalization yields the corresponding tropical graph curve and in this case, solves a topological version of the tropical lifting problem associated to canonically embedded graph curves. We also show that the set of tropical graph curves that we construct are connected via certain local operations. These local operations are inspired by Steinitz’ theorem in polytope theory.

Enabling genome editing in tropical maize lines through an improved, morphogenic regulator-assisted transformation protocol.

The recalcitrance exhibited by many maize (Zea mays) genotypes to traditional genetic transformation protocols poses a significant challenge to the large-scale application of genome editing (GE) in this major crop species. Although a few maize genotypes are widely used for genetic transformation, they prove unsuitable for agronomic tests in field trials or commercial applications. This challenge is exacerbated by the predominance of transformable maize lines adapted to temperate geographies, despite a considerable proportion of maize production occurring in the tropics. Ectopic expression of morphogenic regulators (MRs) stands out as a promising approach to overcome low efficiency and genotype dependency, aiming to achieve 'universal' transformation and GE capabilities in maize. Here, we report the successful GE of agronomically relevant tropical maize lines using a MR-based, Agrobacterium-mediated transformation protocol previously optimized for the B104 temperate inbred line. To this end, we used a CRISPR/Cas9-based construct aiming at the knockout of the VIRESCENT YELLOW-LIKE (VYL) gene, which results in an easily recognizable phenotype. Mutations at VYL were verified in protoplasts prepared from B104 and three tropical lines, regardless of the presence of a single nucleotide polymorphism (SNP) at the seed region of the VYL target site in two of the tropical lines. Three out of five tropical lines were amenable to transformation, with efficiencies reaching up to 6.63%. Remarkably, 97% of the recovered events presented indels at the target site, which were inherited by the next generation. We observed off-target activity of the CRISPR/Cas9-based construct towards the VYL paralog VYL-MODIFIER, which could be partly due to the expression of the WUSCHEL (WUS) MR. Our results demonstrate efficient GE of relevant tropical maize lines, expanding the current availability of GE-amenable genotypes of this major crop.

Classifying tree topology changes along tropical line segments

Classifying tree topology changes along tropical line segments

Tropical Geometric Variation of Tree Shapes

We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is given by the tree’s branching configuration and leaf labeling. We use the tropical line segment as a framework to define notions of variance as well as invariance of tree topologies: we provide a combinatorial search theorem that describes all tree topologies occurring along a tropical line segment, as well as a setting under which tree topologies do not change along a tropical line segment. Our study is motivated by comparison to the moduli space endowed with a geodesic metric proposed by Billera, Holmes, and Vogtmann (referred to as BHV space); we consider the tropical geometric setting as an alternative framework to BHV space for sets of phylogenetic trees. We give an algorithm to compute tropical line segments which is lower in computational complexity than the fastest method currently available for BHV geodesics and show that its trajectory behaves more subtly: while the BHV geodesic traverses the origin for vastly different tree topologies, the tropical line segment bypasses it.

Point line geometry in the tropical plane

We study the classical result by Bruijn and Erdős regarding the bound on the number of lines determined by a n-point configuration in the plane, and in the light of the recently proven Tropical Sylvester-Gallai theorem, come up with a tropical version of the above-mentioned result. In this work, we introduce stable tropical lines, which help in answering questions pertaining to incidence geometry in the tropical plane. Projective duality in the tropical plane helps in translating the question for stable lines to stable intersections that have been previously studied in depth. Invoking duality between Newton subdivisions and line arrangements, we are able to classify stable intersections with shapes of cells in subdivisions, and this ultimately helps us in coming up with a bound. In this process, we also encounter various unique properties of linear Newton subdivisions which are dual to tropical line arrangements.

Tropical Lines on Cubic Surfaces

Tropical Lines on Cubic Surfaces

Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries

Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement, towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement.

Tree Topologies along a Tropical Line Segment

Tropical geometry with the max-plus algebra has been applied to statistical learning models over tree spaces because geometry with the tropical metric over tree spaces has some nice properties such as convexity in terms of the tropical metric. One of the challenges in applications of tropical geometry to tree spaces is the difficulty interpreting outcomes of statistical models with the tropical metric. This paper focuses on combinatorics of tree topologies along a tropical line segment, an intrinsic geodesic with the tropical metric, between two phylogenetic trees over the tree space and we show some properties of a tropical line segment between two trees. Specifically we show that a probability of a tropical line segment of two randomly chosen trees going through the origin (the star tree) is zero if the number of leave is greater than four, and we also show that if two given trees differ only one nearest neighbor interchange (NNI) move, then the tree topology of a tree in the tropical line segment between them is the same tree topology of one of these given two trees with possible zero branch lengths.

Large-scale reconstruction of chromatin structures of maize temperate and tropical inbred lines.

Maize is a model plant species often used for genetics and genomics research because of its genetic diversity. There are prominent morphological, genetic, and epigenetic variations between tropical and temperate maize lines. However, the genome-wide chromatin conformations of these two maize types remain unexplored. We applied a Hi-C approach to compare the genome-wide chromatin interactions between temperate inbred line D132 and tropical line CML288. A reconstructed maize three-dimensional genome model revealed the spatial segregation of the global A and B compartments. The A compartments contain enriched genes and active epigenome marks, whereas the B compartments are gene-poor, transcriptionally silent chromatin regions. Whole-genome analyses indicated that the global A compartment content of CML288 was 3.12% lower than that of D132. Additionally, global and A/B sub-compartments were associated with differential gene expression and epigenetic changes between two inbred lines. About 25.3% of topologically associating domains (TADs) were determined to be associated with complex domain-level modifications that induced transcriptional changes, indicative of a large-scale reorganization of chromatin structures between the inbred maize lines. Furthermore, differences in chromatin interactions between the two lines correlated with epigenetic changes. These findings provide a solid foundation for the wider plant community to further investigate the genome-wide chromatin structures in other plant species.

Agro-morphological Characterization of Maize (Zea mays L.) Hybrids Under Acid Soils in Two Contrasting Environments

Acidic soils cover 75 to 80% of the arable soils in the humid forest areas of Cameroon, causing maize yield losses of around 69%. Sixty-four accessions of maize hybrids were developped from “Line × Tester” crosses between twenty tropical inbred lines with three testers (Cam inbgp117, 88069 and 9450) and between testers themselves, and one acid tolerant open pollinated variety (ATP-SR-Y). Those inbred breeding lines were collected from CIMMYT, IITA and IRAD and the derived single hybrids were characterized using agro-morphological maize’s descriptors on a completely randomized block design in two contrasting environments (Nkoemvone and Nkolbisson). The data collected was subjected to multivariate analyses. The Principal Component Analysis showed the first two components being 73.60% and 78.99% of the total variation in Nkoemvone and Nkolbisson, respectively. Furthermore, grain yield showed a positive and highly significant correlation with the plant emergence rate in Nkoemvone (r = 0.61, P < 0.001) and Nkolbisson (r = 0.84, P < 0.001). Hierarchical Clustering Analysis indicated that these accessions forms four distinct groups, where each of the groups showed clear specific features for which the performance differs from that of the others in Nkoemvone and Nkolbisson. Characters such as plant emergence rate, prolificacy, ear appearance and grain yield have been found as important phenotypic markers for assessing agromorphological diversity of maize hybrids. These traits should necessarily be considered in maize breeding programs for varietal discrimination and formulation of cores collection of maize tolerant to aluminum and manganese toxicities in the soil.

Assessment of genetic gains from introgression of temperate genes into tropical elite maize inbred lines: I. performance per se

There is very limited information on genetic gains and improvement of maize inbred line performance per se that has been attained through introgression of temperate germplasm into tropical maize germplasm to enhance adaptability in target environments. The objective of this study was to determine the genetic gains for grain yield and its components achieved by introgression of temperate germplasm into tropical elite maize inbred lines. A total of 123 maize inbred lines comprising of 76 introgressed inbred lines, 21 tropical inbred lines (negative controls) and 26 temperate inbred lines (positive controls) were evaluated in an augmented design at four sites. The strategy was effective and successful to enhance grain yield, in particular, ear prolificacy. Positive genetic gains were realised for grain yield (5%) and ear prolificacy (46%) relative to the population and mean of checks. Selection for plant and ear height, root and stalk lodging had gains ranging from 2 to 11%. However, traits such as anthesis and silking days and grain moisture content at harvest had low gains. Introgressed inbred line performance per se was impressive because new inbred lines with potential for commercial production were obtained. Inbred line 71-DMLF7_88 showed combined early physiological maturity, high ear prolificacy and grain yield potential that were at par with the mean of the temperate checks. Thus, indicating an improvement in the agronomic performance of the improved tropical based material that normally performs below temperate checks in South African warm temperate environments. In conclusion, introgression of temperate germplasm into tropical elite inbred lines was effective in improving adaptation in warm temperate environments.

Assessment of genetic gains for grain yield and components from introgression of temperate donor inbred line into tropical elite maize inbred lines: II. Performance inter se

In maize breeding programs, temperate germplasm can be used to introgress genes from temperate inbred lines into elite tropical maize inbred lines to improve grain yield and its components across environments. This study's objective was to determine the genetic gains for grain yield and its components achieved by the introgression of temperate maize germplasm in tropical elite maize inbred lines for adaptability to South African environments. One hundred and twenty-two Introgressed inbred lines developed using the pedigree breeding method were crossed to four tropical elite inbred line testers using a line x tester mating design to obtain 488 experimental single cross hybrids. Subject to availability of adequate seed for evaluation, a panel of 444 experimental single-cross hybrids were evaluated using an augmented design in two experiments defined as populations A and B at three sites in South African environments. Grain yield and ear prolificacy had positive realized genetic gains of up to 58 and 26%, respectively, relative to the panel mean and commercial check hybrids. Secondary traits, such as anthesis and silking days, had gains ranging from 1 to 37%. Negligible gains were attained for stalk and root lodging and grain moisture content at harvest. Despite the need for further improvement, introgressed inbred lines performance inter se indicated significant grain yield potential improvements following one breeding cycle. The following experimental single-cross hybrids 12C22785, 12C20628, 11C1774, 12C20264, 12C20595, 11C1645 13XH349 outperformed the best commercial check hybrid PAN6Q445B, a leading hybrid on the South African market for grain yield performance potential. These seven selected single-cross hybrids also combined high grain yield potential performance with good ear prolificacy, in particular, experimental single-cross hybrids 12C20628, 11C1774 and 12C202595. Two experimental single-cross hybrids 12C2064 and 13XH349, combined high grain yield performance potential with low grain moisture content at harvest and improved standing ability relative to commercial check hybrids. Parents of these selected experimental single-cross hybrids will be advanced in the breeding program and will be the basis of future breeding for adaptation to South African environments. However, the general trend showed that many of the selected experimental single-cross hybrids did perform poorly for standability data depicted by plant aspects such as plant and ear height, stalk, and root lodging. Therefore, there is a need to improve these plants further to enhance the adaptability of tropical germplasm in South African environments. In conclusion, the introgression strategy effectively enhanced tropical elite inbred lines for the desired economic traits, to the extent that several of their combinations resulted in superior hybrids that are highly desired for South African markets.

Short communication: Finetuning molecular markers for efficient selection of vitamin A-rich tropical maize lines in a molecular breeding scheme

Short communication: Finetuning molecular markers for efficient selection of vitamin A-rich tropical maize lines in a molecular breeding scheme

Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight

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.

Exploring the potential usefulness of U.S. maize expired Plant Variety Protection Act lines for maize breeding in sub‐Saharan Africa

AbstractMaize (Zea mays L.) inbred lines with expired Plant Variety Protection Act (ExPVP) certificates are publicly available and potentially represent a new germplasm resource for many public and private breeding programs. The use of these inbred lines for maize breeding in sub‐Saharan African (SSA) was little investigated. Hence, this study was conducted to explore their potential usefulness. Ninety‐six ExPVP lines, two temperate public lines, and 14 tropical lines were evaluated in five different trials from 2016 to 2018 in Burkina Faso to determine their phenotypic characteristics; resistance to drought, heat, and three diseases; and to identify elite ExPVP lines for local maize breeding programs. Cluster analysis based on phenotypic traits highlighted a clear distinction between the different groups (nonstiff stalk [NS] vs. Iowa Stiff Stalk Synthetic [SS] heterotic groups and temperate vs. tropical germplasms). The screening showed that 3, 28, and 68% of ExPVP lines were resistant, tolerant, and susceptible to maize leaf blight disease, respectively. However, the lines were either tolerant or resistant to Curvularia leaf spot and maize streak virus. Approximately 30% of ExPVP lines presented a tolerance to the three maize diseases tested and 8% of the lines were tolerant to drought. Heat stress was severe to both ExPVP and tropical lines. Yield potential of ExPVP lines varied from 1.68 to 2635.63 kg ha−1 vs. 798.76 to 1707.56 kg ha−1 for tropical lines. The ExPVP lines identified showing tolerance to stresses and a high‐yield performance can be integrated in inbred‐hybrid development program.

Evaluation of U.S. inbred lines with expired plant variety protection for mid-altitude tropical maize breeding

Maize (Zea mays L.) inbred lines with expired U.S. Plant Variety Protection Act certificates (ex-PVPA) can be an important source of favorable alleles to improve grain yield, root and stalk lodging, drydown, plant architecture, and reduced time to maturity of tropical hybrids. Understanding the heterotic patterns and combining ability of ex-PVPA lines with tropical lines is necessary to design effective breeding strategies using this germplasm. This study evaluated 10 Iowa Stiff Stalk Synthetic (BSSS) and 11 Non-Stiff Stalk Synthetic (NSSS) inbred lines in hybrid combinations with tropical mid-altitude testers in five mid-altitude environments (900–2000 masl) in Mexico and identified six hybrids with grain yield equal or superior to that of the check hybrids. Two NSSS inbred lines: PHR03 and PHN82 had significant (P < 0.01) and positive general combining ability (GCA) effects with inbred lines from CIMMYT’s Tuxpeno heterotic group. Similarly, the BSSS line PHG39 had a significant positive GCA effect (P < 0.05) with non-Tuxpeno lines. The lines PHN82 and PHK29 had positive GCA effects (P < 0.01) under drought stress and could be used as sources of drought tolerance in CIMMYT breeding programs. The mid-altitude lines CML537 and CML539 had positive GCA effects (1.45 and 0.69 t/ha, respectively; P < 0.01) with NSSS lines whereas hybrids of CML384 with BSSS lines yielded 0.64 t/ha (P < 0.01) more than the average of the testcrosses. These results showed that U.S. ex-PVPA lines can increase grain yield of CIMMYT’s tropical mid-altitude hybrids.

Genomic-wide association study for white spot resistance in a tropical maize germplasm

White spot is an important maize disease, prevalent in most high production tropical regions with a severe negative impact in grain yield. Breeding for white spot resistance is the most effective mechanism to control the disease. The objectives of this research include identifying and mapping chromosomal regions and putative genes associated to the maize response to white spot. We performed an association mapping with phenotypic data collected in two environments located at South region of Brazil, and by using a set of 355,972 high-quality single nucleotide polymorphism markers in a panel composed by 183 tropical field corn and popcorn inbred lines. Nine SNPs were significantly associated with white spot, five of them co-localized on previously reported quantitative trait loci regions, while remaining regions are novel. The total phenotypic variance explained (r2) by the nine SNPs associated with white spot severity was 64.3%, while the variance explained by each SNP ranged from 0.72 to 25.54%. The identified putative gene models are promising candidates associated with white spot resistance. Once these SNPs were validated, they can be useful for selecting superior genotypes.

Testers in supersweet corn lines

ABSTRACT: The purpose of this study was to evaluate the discriminatory capacity of tester lines for tropical corn lines converted to supersweet shrunken (sh2) gene, for the development of hybrids adapted to tropical conditions. Lines were used as female parents in crosses with three testers: open-pollinated mixed variety; supersweet line L4; supersweet commercial hybrid Tropical Plus. Four trials were carried out to evaluate topcrosses in Maringá - PR e Sabáudia - PR, Brazil in the main growing season of 2015/16. The following traits were evaluated: total ear weight (TEW, in kg), commercial ear weight (CEW, in kg) and total soluble solids (TSS, in °Brix). The GCA estimates for TEW and CEW were highest for L4. The lines Balu-114 and UEM-25 were selected based on the effects of g ̂ ifor the traits studied and should be used in the establishment of base populations for the breeding of superior lines. The s ̂ ijvalue for TEW was highest for cross BALU-182 x Tropical, while for CEW was the highest value for cross BALU-94 x Mista.

The impact of climate change on the Australian sugarcane industry

Abstract This study assesses the impact of climate change on changes in sugarcane output for Australia’s main sugarcane-growing regions, using a dataset for the years 1964–2012. We test for accelerated effects of climate change post-1995 (the midpoint in our testing period), as well as for possible non-linear impacts of climate change that are related to the geographical location of sugarcane plantations. Our findings show that increases in atmospheric carbon concentration have had a significant negative impact on sugarcane output after 1995, which contrasts with an earlier positive effect before 1995. Peak temperatures also had a larger impact on sugarcane output after 1995. For areas south of the tropical line and from 1995 onwards, an extra kilometer of distance from the tropical line corresponds to an increase of 1 million tons in sugarcane output growth. Our study tests for additional variables (irrigation, sugarcane diseases, fertilizer use, and dominant sugarcane variety planted) with results remaining similar. We conclude by discussing implications for policymakers and future research, in particular, the importance of factoring in regional differences and non-linear effects into adaptation planning across agricultural regions.