QTL mapping for maize resistance and yield under infestation with Sesamia nonagrioides

The Mediterranean corn borer (MCB) is the most important maize insect pest in the Mediterranean region. The main objective was to map quantitative trait loci (QTL) for yield performance under infestation with MCB, resistance and agronomic traits in a maize RIL population derived from an inbred cross European flint × Reid. Six QTL for resistance traits were located: one QTL for tunnel length (bin 9.03; p = 19.8 %), one QTL for stalk lodging (bin 3.07, p = 11.5 %), and four QTL for ear resistance (bins 1.07, 5.03/5.05, and 8.04; p = 25–63 %). Twelve QTL for agronomic traits were located: a QTL for yield under infestation (bin 5.03, p = 15 %); two QTL for grain moisture (bins 1.07 and 8.05); two QTL for days to anthesis (bin 1.07 and 8.05); two QTL for days to silking (bins 8.04 and 10.02); three QTL for plant height (bins 5.04, 8.05 and 9.03); and two QTL for ear height (bins 8.05 and 9.03). No genetic correlations between yield and other traits were observed. The cross validation (CV) approach showed that the estimation biases for QTL for resistance traits were higher than those for agronomic traits. This work stresses the importance of the region 9.03 for controlling corn borer resistance and suggests the presence of QTL with small effect on ear-resistance traits. At the same genomic region, there are also genes that control plant and ear height and future works could elucidate whether these genes are the same or are closely linked. The QTL for yield seem to play an important role in MCB tolerance in this genetic background. Large biases observed for QTL effects by CV were mainly due to the small sample size used and were higher for resistance traits due to their larger genetic complexity. We consider that it is more appropriate to select for grain yield under infestation instead of selecting for resistance traits because resistance to MCB could have unfavorable associations with agronomic traits.     

Do large effect QTL fractionate? A case study at the maize domestication QTL teosinte branched1

Quantitative trait loci (QTL) mapping is a valuable tool for studying the genetic architecture of trait variation. Despite the large number of QTL studies reported in the literature, the identified QTL are rarely mapped to the underlying genes and it is usually unclear whether a QTL corresponds to one or multiple linked genes. Similarly, when QTL for several traits colocalize, it is usually unclear whether this is due to the pleiotropic action of a single gene or multiple linked genes, each affecting one trait. The domestication gene teosinte branched1 (tb1) was previously identified as a major domestication QTL with large effects on the differences in plant and ear architecture between maize and teosinte. Here we present the results of two experiments that were performed to determine whether the single gene tb1 explains all trait variation for its genomic region or whether the domestication QTL at tb1 fractionates into multiple linked QTL. For traits measuring plant architecture, we detected only one QTL per trait and these QTL all mapped to tb1. These results indicate that tb1 is the sole gene for plant architecture traits that segregates in our QTL mapping populations. For most traits related to ear morphology, we detected multiple QTL per trait in the tb1 genomic region, including a large effect QTL at tb1 itself plus one or two additional linked QTL. tb1 is epistatic to two of these additional QTL for ear traits. Overall, these results provide examples for both a major QTL that maps to a single gene, as well as a case in which a QTL fractionates into multiple linked QTL.     

Epistatic interaction is an important genetic basis of grain yield and its components in maize

A population of 294 recombinant inbred lines (RIL) derived from Yuyu22, an elite maize hybrid extending broadly in China, has been constructed to investigate the genetic basis of grain yield, and associated yield components in maize. The main-effect quantitative trait loci (QTL), digenic epistatic interactions, and their interactions with the environment for grain yield and its three components were identified by using the mixed linear model approach. Thirty-two main-effect QTL and forty-four pairs of digenic epistatic interactions were detected for the four measured traits in four environments. Our results suggest that both additive effects and epistasis (additive × additive) effects are important genetic bases of grain yield and its components in the RIL population. Only 30.4% of main-effect QTL for ear length were involved in epistatic interactions. This implies that many loci in epistatic interactions may not have significant effects for traits alone but may affect trait expression by epistatic interaction with the other loci.     

High-density linkage mapping of yield components and epistatic interactions in maize with doubled haploid lines from four crosses

Grain yield (GY) is a genetically complex and physiologically multiplicative trait which can be decomposed into the components kernel number (KN) and 100-kernel weight (HKW). Genetic analysis of these less complex yield component traits may give insights into the genetic architecture and predictive ability of complex traits. Here, we investigated how the incorporation of component traits and epistasis in quantitative trait locus (QTL) mapping approaches influences the accuracy of GY prediction. High-density genetic maps with 7,000–10,000 polymorphic single nucleotide polymorphisms were constructed for four biparental populations. The populations comprised between 99 and 227 doubled haploid maize lines which were phenotyped in field trials in two environments. Heritability was highest for HKW (88–89 %), intermediate for KN (72–80 %), and lowest for GY (64–83 %). Mapped QTL explained in total 21–55 %, 22–67 %, and 24–75 % of the genotypic variance for GY, KN, and HKW, respectively. Support intervals of QTL were short, indicating that QTL were located with high precision. Co-located QTLs with same parental origin of favorable alleles were detected within populations for different traits and between populations for the same traits. Using GY predictions based on the detected QTL, prediction accuracies (r) determined by cross validation ranged from 0.18 to 0.52. Epistatic models did not outperform the corresponding additive models. In conclusion, models based on QTL positions of component traits support the identification of favorable alleles for multiplicative traits and provide a basis to select superior inbred lines by marker-assisted breeding.     

玉米雌穗发育期基因差异表达与杂种优势的研究

杂种优势在提高粮食作物特别是玉米的产量方面具有重要的作用。然而,杂种优势的原理却仍然是一个世界性的难题。用12个玉米自交系及其按不完全双列杂交组配的33个杂交种为材料,分4个不同发育时期取杂交种及其亲本的雌穗组织,利用差异显示技术,分析杂种与亲本的基因差异表达类型及其与7个主要农艺性状的杂种表现和杂种优势的相关关系。发现1):在5种表达类型中单态表达(基因在杂交种和双亲中同时表达的类型)的数量最大,这说明杂种优势的形成不仅与基因的表达与否相关,还与大量基因的上调或下调表达相关;2):在玉米雌幼穗的发育初期杂交种与双亲的基因表达差异最大,这可能与雌穗发育初期器官的形成和发育相关,因此这一时期差异表达(在质的方面)的基因对产量性状和杂种优势的形成具有密切关系;3):综合各种基因表达类型与产量性状和杂种优势的关系,发现某些基因在杂种中的沉默表达可以促进籽粒的发育和抑制幼穗中小花的发育。     

Spatial and temporal expression modes of MicroRNAs in an elite rice hybrid and its parental lines

Heterosis is a commonly observed phenomenon in nature and refers to the superior performance of hybrids relative to both parents. The molecular mechanisms of heterosis are mostly unknown. Quantitative trait locus (QTL) mapping has been used to explain the genetic basis of heterosis, and large amounts of QTLs have been mapped for various agronomic traits, but the nature of QTL contributing to heterosis is still enigmatic. MicroRNAs (miRNAs) are master regulators in the processes of plant development and trait performance, and many miRNAs are predicted to reside in QTL intervals. We analyzed the expression modes of miRNAs, which were picked up from miRNA databases and chosen from those predicted from QTL intervals by bioinformatic approaches, in different organs at developmental stages of an elite rice hybrid and its parents. All possible modes of action for miRNA expression were detected, but most miRNAs showed nonadditive mode, and different stages and distinct organs displayed different patterns of miRNA expression. A large proportion of miRNAs were not detected for expression in leaves but expressed in the culms and roots of the hybrid at tillering stage. MiRNAs from grain-weight QTL intervals have multiple effects on grain development. Together, our results reveal that miRNAs, especially those from QTL intervals, play roles in heterotic performance in this elite rice hybrid, our results also shade new light on understanding the molecular mechanisms of heterosis.     

Identification of Genetic Factors Contributing to Heterosis in a Hybrid from Two Elite Maize Inbred Lines Using Molecular Markers

The use of molecular markers to identify quantitative trait loci (QTLs) affecting agriculturally important traits has become a key approach in plant genetics-both for understanding the genetic basis of these traits and to help design novel plant improvement programs. In the study reported here, we mapped QTLs (and evaluated their phenotypic effects) associated with seven major traits (including grain yield) in a cross between two widely used elite maize inbred lines, B73 and Mo17, in order to explore two important phenomena in maize genetics-heterosis (hybrid vigor) and genotype-by-environment (G x E) interaction. We also compared two analytical approaches for identifying QTLs, the traditional single-marker method and the more recently described interval-mapping method. Phenotypic evaluations were made on 3168 plots (nearly 100,000 plants) grown in three states. Using 76 markers that represented 90-95% of the maize genome, both analytical methods showed virtually the same results in detecting QTLs affecting grain yield throughout the genome, except on chromosome 6. Fewer QTLs were detected for other quantitative traits measured. Whenever a QTL for grain yield was detected, the heterozygote had a higher phenotype than the respective homozygote (with only one exception) suggesting not only overdominance (or pseudooverdominance) but also that these detected QTLs play a significant role in heterosis. This conclusion was reinforced by a high correlation between grain yield and proportion of heterozygous markers. Although plant materials were grown and measured in six diverse environments (North Carolina, Iowa and Illinois) there was little evidence for G x E interaction for most QTLs.     

Genetic relationships between resistance to stalk-tunneling by the European corn borer and cell-wall components in maize population B73×B52

The objective of this study was to assess the relationships among quantitative trait loci (QTL) detected for European corn borer (ECB) tunneling and cell-wall components (CWC) neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL) content in leaf-sheath and stalk tissues in a maize recombinant inbred line population derived from inbred lines B73 and B52. Most of the QTL for ECB resistance (10/13) were at QTL positions for one or more CWC. Of the 12 QTL for NDF and ADF in leaf-sheaths, five for each trait were at or near QTL for ECB tunneling. Four of these five QTL for NDF and ADF mapped to common locations. Four of the eight leaf-sheath ADL QTL were detected in the same genomic regions as ECB QTL. For stalk tissue, four regions contained common/overlapping QTL for ECB tunneling, NDF, and ADF. Six such regions were observed for stalk ADL and ECB tunneling. Seven of the ten QTL associated with both CWC and ECB tunneling contributed to the negative correlations observed between these traits, while relatively few QTL effects were positively correlated. This suggests that while CWC contribute to ECB resistance in this population, other mechanisms and other genes also are involved. Several QTL contributing to the negative correlations between ECB tunneling and CWC in the leaf-sheaths mapped to similar positions as QTL detected in tropical maize populations for resistance to leaf-feeding by Diatraea grandiosella Dyar and Diatraea saccharalis Fabricus. These regions may contain genes involved in the synthesis of cellulose, hemicellulose, and lignin in the leaf-blades and leaf-sheaths of maize.     

Confirming quantitative trait loci for aflatoxin resistance from Mp313E in different genetic backgrounds

The fungus Aspergillus flavus (Link:Fr) causes ear rot of maize (Zea mays L.) and produces the toxic metabolic product aflatoxin. One particularly effective method of controlling the fungus is via host plant resistance, but while several resistant breeding lines have been identified, transferring the resistance genes from these lines into elite cultivars has been less effective than needed. A high number of genes involved with resistance, each with a small effect, and some only found under certain environmental conditions, has hampered resistance breeding. The identification of markers linked to genomic regions associated with resistance would aid in this effort. The goals of this study were to identify and characterize quantitative trait loci (QTL) conferring resistance to aflatoxin accumulation from resistant maize donor Mp313E in a background of the susceptible inbred line Va35; to compare them to the QTL identified from Mp313E in a background of B73; and to test the stability of the QTL identified in Mp313E × Va35 in multiple environments by remapping the phenotypic tails of the Mp313E × Va35 mapping population in new locations. Twenty different QTL were found in this study, 11 of which were also found in different environments using the phenotypic tail subset mapping population, and five of which were likely the same as those reported in the Mp313E × B73 mapping population. This indicates that many of the QTL are stable over the environments and genetic backgrounds tested, which will make them more valuable in breeding efforts.     

玉米株高和穗位高的遗传基础与分子机制*

株高和穗位高是玉米重要育种性状,直接影响植株的养分利用效率及抗倒伏性,进而影响玉米产量。玉米株高和穗位高属于典型数量性状,目前通过数量性状位点(quantitative trait loci mapping,QTL)定位和全基因组关联分析(genome-wide association study, GWAS)等方法已挖掘到较多相关遗传位点,通过QTL精细定位及利用突变体克隆了一些调控株高和穗位高关键基因。但是由于各研究组所利用的群体类型和大小、标记类型和密度以及统计方法不同,所鉴定QTL差异较大,单个研究难以揭示玉米株高和穗位高遗传结构。早期QTL定位的结果多以遗传距离来展示,不同时期GWAS研究所使用参考基因组版本不同,这进一步增加了借鉴和利用前人研究结果的难度。首次将目前已鉴定株高和穗位高遗传定位信息统一锚定至玉米自交系B73参考基因组V4版本,构建了株高和穗位高性状定位的一致性图谱,并鉴定出可被多个独立研究定位的热点区间。进一步对已克隆玉米株高和穗位高调控基因进行总结与分类,揭示株高和穗位高性状调控机制,对深度解析株高和穗位高遗传结构、指导基因克隆和利用分子标记辅助选择优化玉米株高和穗位高性状均具有重要意义。     

Classical genetic and quantitative trait loci analyses of heterosis in a maize hybrid between two elite inbred lines

The exploitation of heterosis is one of the most outstanding advancements in plant breeding, although its genetic basis is not well understood yet. This research was conducted on the materials arising from the maize single cross B73 x H99 to study heterosis by procedures of classical genetic and quantitative trait loci (QTL) analyses. Materials were the basic generations, the derived 142 recombinant inbred lines (RILs), and the three testcross populations obtained by crossing the 142 RILs to each parent and their F(1). For seedling weight (SW), number of kernels per plant (NK), and grain yield (GY), heterosis was >100% and the average degree of dominance was >1. Epistasis was significant for SW and NK but not for GY. Several QTL were identified and in most cases they were in the additive-dominance range for traits with low heterosis and mostly in the dominance-overdominance range for plant height (PH), SW, NK, and GY. Only a few QTL with digenic epistasis were identified. The importance of dominance effects was confirmed by highly significant correlations between heterozygosity level and phenotypic performance, especially for GY. Some chromosome regions presented overlaps of overdominant QTL for SW, PH, NK, and GY, suggesting pleiotropic effects on overall plant vigor.     

Genetic Architecture of Ear Fasciation in Maize (Zea mays) under QTL Scrutiny

Maize ear fasciation

Knowledge of the genes affecting maize ear inflorescence may lead to better grain yield modeling. Maize ear fasciation, defined as abnormal flattened ears with high kernel row number, is a quantitative trait widely present in Portuguese maize landraces.

Material and Methods

Using a segregating population derived from an ear fasciation contrasting cross (consisting of 149 F_2:3 families) we established a two location field trial using a complete randomized block design. Correlations and heritabilities for several ear fasciation-related traits and yield were determined. Quantitative Trait Loci (QTL) involved in the inheritance of those traits were identified and candidate genes for these QTL proposed.

Results and Discussion

Ear fasciation broad-sense heritability was 0.73. Highly significant correlations were found between ear fasciation and some ear and cob diameters and row number traits. For the 23 yield and ear fasciation-related traits, 65 QTL were identified, out of which 11 were detected in both environments, while for the three principal components, five to six QTL were detected per environment. Detected QTL were distributed across 17 genomic regions and explained individually, 8.7% to 22.4% of the individual traits or principal components phenotypic variance. Several candidate genes for these QTL regions were proposed, such as bearded-ear1, branched silkless1, compact plant1, ramosa2, ramosa3, tasselseed4 and terminal ear1. However, many QTL mapped to regions without known candidate genes, indicating potential chromosomal regions not yet targeted for maize ear traits selection.

Conclusions

Portuguese maize germplasm represents a valuable source of genes or allelic variants for yield improvement and elucidation of the genetic basis of ear fasciation traits. Future studies should focus on fine mapping of the identified genomic regions with the aim of map-based cloning.     

Genetic mapping and QTL analysis for yield and agronomic traits with an F2:3 population derived from a waxy corn × sweet corn cross

We constructed a framework map using SSR markers in the F₂ population derived from a cross between a waxy corn inbred line and a sweet corn inbred line. We constructed a genetic linkage map of the F_2:3 population employing 295 SSR markers on 158 F₂ individuals produced from the cross. The map comprised a total genomic length of 2,626.5 cM in 10 linkage groups and an average distance between markers of 8.9 cM. The number of loci per linkage group ranged from 27 (chr. 5) to 34 (chr. 7). The genetic distance per linkage group ranged from 213.6 cM (chr. 10) to 360.6 cM (chr. 2). Χ ² tests revealed that 254 markers (86.1 %) distributed over all 10 chromosomes exhibited a Mendelian segregation ratio of 1:2:1. A total of 14 quantitative trait loci (QTLs) for days to silking (DTS), plant height (PH), ear height (EH), ear height ratio (ER), ear length (L-ear), and setted ear length (L-sear) were found in the 158 F₂ progeny. They were mapped to chromosomes 1, 2, 3, 7, 8, and 10. Among them, one QTL was associated with DTS, three with PH, six with EH, one with ER, two with L-ear, and one QTL was related to L-sear. In our study, we found that four QTLs: qDTS1, qEH1a, qEH1b, and qPH1, were clustered between umc2390 and umc1603 on chromosome 1. These new QTLs identified by the present study could serve as useful molecular markers in selecting for yield and agronomic traits in maize. The results of this study may improve the identification and characterization of genes responsible for yield and agronomic traits in waxy corn and sweet corn.     

Genetic architecture controlling variation in grain carotenoid composition and concentrations in two maize populations

Key message

Genetic control of maize grain carotenoid profiles is coordinated through several loci distributed throughout three secondary metabolic pathways, most of which exhibit additive, and more importantly, pleiotropic effects.

Abstract

The genetic basis for the variation in maize grain carotenoid concentrations was investigated in two F_2:3 populations, DEexp × CI7 and A619 × SC55, derived from high total carotenoid and high β-carotene inbred lines. A comparison of grain carotenoid concentrations from population DEexp × CI7 grown in different environments revealed significantly higher concentrations and greater trait variation in samples harvested from a subtropical environment relative to those from a temperate environment. Genotype by environment interactions was significant for most carotenoid traits. Using phenotypic data in additive, environment-specific genetic models, quantitative trait loci (QTL) were identified for absolute and derived carotenoid traits in each population, including those specific to the isomerization of β-carotene. A multivariate approach for these correlated traits was taken, using carotenoid trait principal components (PCs) that jointly accounted for 97 % or more of trait variation. Component loadings for carotenoid PCs were interpreted in the context of known substrate-product relationships within the carotenoid pathway. Importantly, QTL for univariate and multivariate traits were found to cluster in close proximity to map locations of loci involved in methyl-erythritol, isoprenoid and carotenoid metabolism. Several of these genes, including lycopene epsilon cyclase, carotenoid cleavage dioxygenase1 and beta-carotene hydroxylase, were mapped in the segregating populations. These loci exhibited pleiotropic effects on α-branch carotenoids, total carotenoid profile and β-branch carotenoids, respectively. Our results confirm that several QTL are involved in the modification of carotenoid profiles, and suggest genetic targets that could be used for the improvement of total carotenoid and β-carotene in future breeding populations.     

The genetic architecture of amino acids dissection by association and linkage analysis in maize

Amino acids are both constituents of proteins, providing the essential nutrition for humans and animals, and signalling molecules regulating the growth and development of plants. Most cultivars of maize are deficient in essential amino acids such as lysine and tryptophan. Here, we measured the levels of 17 different total amino acids, and created 48 derived traits in mature kernels from a maize diversity inbred collection and three recombinant inbred line (RIL) populations. By GWAS, 247 and 281 significant loci were identified in two different environments, 5.1 and 4.4 loci for each trait, explaining 7.44% and 7.90% phenotypic variation for each locus in average, respectively. By linkage mapping, 89, 150 and 165 QTLs were identified in B73/By804, Kui3/B77 and Zong3/Yu87‐1 RIL populations, 2.0, 2.7 and 2.8 QTLs for each trait, explaining 13.6%, 16.4% and 21.4% phenotypic variation for each QTL in average, respectively. It implies that the genetic architecture of amino acids is relative simple and controlled by limited loci. About 43.2% of the loci identified by GWAS were verified by expression QTL, and 17 loci overlapped with mapped QTLs in the three RIL populations. GRMZM2G015534, GRMZM2G143008 and one QTL were further validated using molecular approaches. The amino acid biosynthetic and catabolic pathways were reconstructed on the basis of candidate genes proposed in this study. Our results provide insights into the genetic basis of amino acid biosynthesis in maize kernels and may facilitate marker‐based breeding for quality protein maize.     

Mapping QTL for grain yield and other agronomic traits in post-rainy sorghum [Sorghum bicolor (L.) Moench]

Sorghum, a cereal of economic importance ensures food and fodder security for millions of rural families in the semi-arid tropics. The objective of the present study was to identify and validate quantitative trait loci (QTL) for grain yield and other agronomic traits using replicated phenotypic data sets from three post-rainy dry sorghum crop seasons involving a mapping population with 245 F₉ recombinant inbred lines derived from a cross of M35-1 × B35. A genetic linkage map was constructed with 237 markers consisting of 174 genomic, 60 genic and 3 morphological markers. The QTL analysis for 11 traits following composite interval mapping identified 91 QTL with 5–12 QTL for each trait. QTL detected in the population individually explained phenotypic variation between 2.5 and 30.3 % for a given trait and six major genomic regions with QTL effect on multiple traits were identified. Stable QTL across seasons were identified. Of the 60 genic markers mapped, 21 were found at QTL peak or tightly linked with QTL. A gene-based marker XnhsbSFCILP67 (Sb03g028240) on SBI-03, encoding indole-3-acetic acid-amido synthetase GH3.5, was found to be involved in QTL for seven traits. The QTL-linked markers identified for 11 agronomic traits may assist in fine mapping, map-based gene isolation and also for improving post-rainy sorghum through marker-assisted breeding.     

玉米雌穗性状遗传分析与形成机制*

雌穗是玉米重要的生殖器官,雌穗发育决定成熟果穗大小及单穗粒重,进而直接影响玉米产量。雌穗性状主要包括穗长、穗粗、穗行数、行粒数、穗重、单穗粒重等,均为多基因控制的数量遗传性状,且其遗传结构各不相同。解析雌穗性状的遗传基础,优化雌穗结构,是玉米增产的重要途径。前人通过数量性状位点(quantitative trait locus mapping,QTL)定位和全基因组关联分析(genome-wide association study, GWAS)等方法,已经鉴定出较多雌穗性状相关的遗传位点,但是目前已鉴定功能的基因较少,所建立的遗传位点一致性图谱并不完整,因此难以全面揭示雌穗性状遗传结构。通过综合前人雌穗性状遗传定位进展,现将已鉴定QTL位点和显著关联SNP整合至玉米B73参考基因组V4版本,并鉴定出雌穗性状定位热点区间,对深入解析雌穗性状遗传结构、指导雌穗性状基因克隆和理解雌穗发育分子机制均具有重要意义。