A QTL atlas for grain yield and its component traits in maize (Zea mays)

Grain yield and its component traits are essential targets in maize breeding. These traits are genetically complex and controlled by a large number of quantitative trait loci (QTL). The aim of this study was to compile reported QTL and major genes for grain yield and its component traits in a QTL atlas, as a valuable resource for the maize community. To this end, 1,177 QTL related to maize yield were collected from 56 studies published between 1992 and 2018. These QTL were projected to genetic map “IBM2 2008 Neighbors”, which led to the identification of 135 meta-QTL. Some genomic regions appear to be hotspots for yield-related meta-QTL, often affecting more than one of the investigated traits. Moreover, we catalogued 20 major maize loci associated with yield and identified 65 maize homologs of 21 rice yield-related genes. Interestingly, we found that a significant proportion of them are located in meta-QTL regions. Collectively, this study provides a reference for QTL fine-mapping and gene cloning, as well as for molecular marker-assisted breeding of yield-related traits in maize.     

QTL mapping of maize (Zea mays) stay-green traits and their relationship to yield

A maize genetic linkage map derived from 115 simple sequence repeat (SSR) markers was constructed from an F₂ population. The F₂ was generated from a cross between a stay-green inbred line (Q319) and a normal inbred line (Mo17). The map resolved 10 linkage groups and spanned 1431.0 cM in length with an average genetic distance of 12.44 cM between two neighbouring loci. A total of 14 quantitative trait loci (QTL) were detected for stay-green traits at different postflowering time intervals and identified by composite interval mapping. The respective QTL contribution to phenotypic variance ranged from 5.40% to 11.49%, with trait synergistic action from Q319. Moreover, maize stay-green traits were closely correlated to grain yield. Additional QTL analyses indicated that multiple intervals of stay-green QTL overlapped with yield QTL.     

Grain yield and root characteristics of summer maize (Zea mays L.) under shade stress conditions

Low light is a major adversity affecting yield and quality of summer maize in the Huang‐Huai‐Hai region of China. We conducted a field experiment to explore the effects of shading on root development and yield formation in two summer maize hybrids (Zea mays L.), Denghai605 (DH605) and Zhengdan958 (ZD958). The experiment consisted of four treatments (CK: ambient sunlight, S1: shading from tasselling to physiological maturity stage, S2: shading from six‐leaf to tasselling stage, S3: shading from seeding to physiological maturity stage). Shading had a strong impact on the development of roots in the upper soil layer. Shading significantly decreased the root dry weight, root/shoot ratio, root length density, root absorption area and active absorption area. The results showed that treatments in a diminishing sequence of effects on root from S3, S1, S2 to CK. Overall, shading decreased the root morphologic and activity indices, and decreased yield in summer maize. During an average of 2 years, yields of ZD958 in S3, S2 and S1 decreased by 85%, 24% and 55%, yields of DH605 in S3, S2 and S1 decreased by 87%, 26% and 67%, in compare to CK. The results will be useful for hybrid selection and improving cultural practices for enhancing the maize shading resistance in Huang‐Huai‐Hai region.     

Mapping QTLs in breeding for drought tolerance in maize (Zea mays L.)

Summary Grain yield in the maize (Zea mays L) plant is sensitive to drought in the period three weeks either side of flowering. Maize is well-adapted to the use of restriction fragment length polymorphisms (RFLPs) to identify a tight linkage between gene(s) controlling the quantitative trait and a molecular marker. We have determined the chromosomal locations of quantitative trait loci (QTLs) affecting grain yield under drought, anthesis-silking interval, and number of ears per plant. The F₃ families derived from the cross SD34(tolerant) × SD35 (intolerant) were evaluated for these traits in a two replicated experiment. RFLP analysis of the maize genome included non-radioactive DNA-DNA hybridization detection using chemiluminescence. To identify QTLs underlying tolerance to drought, the mean phenotypic performances of F₃ families were compared based on genotypic classification at each of 70 RFLP marker loci. The genetic linkage map assembled from these markers was in good agreement with previously published maps. The phenotypic correlations between yield and other traits were highly significant. In the combined analyses, genomic regions significantly affecting tolerance to drought were found on chromosomes 1,3,5,6, and 8. For yield, a total of 50% of the phenotypic variance could be explained by five putative QTLs. Different types of gene action were found for the putative QTLs for the three traits.     

Phenotypic characterization and validation of provitamin A functional genes in early maturing provitamin A-quality protein maize (Zea mays) inbred lines

The number of drought and low-N tolerant hybrids with elevated levels of provitamin A (PVA) in sub-Saharan Africa could increase when PVA genes are optimized and validated for developed drought and low-N tolerant inbred lines. This study aimed to (a) determine the levels of drought and low-N tolerance, and PVA concentrations in early maturing PVA-quality protein maize (QPM) inbred lines, and (b) identify lines harbouring the crtRB1 and LcyE genes as sources of favourable alleles of PVA. Seventy early maturing PVA-QPM inbreds were evaluated under drought, low-N and optimal environments in Nigeria for two years. The inbreds were assayed for PVA levels and the presence of PVA genes using allele-specific PCR markers. Moderate range of PVA contents was observed for the inbreds. Nonetheless, TZEIORQ 55 combined high PVA concentration with drought and low-N tolerance. The crtRB1-3′TE primer and the KASP SNP (snpZM0015) consistently identified nine inbreds including TZEIORQ 55 harbouring the favourable alleles of the crtRB1 gene. These inbreds could serve as donor parents of the favourable crtRB1-3′TE allele for PVA breeding in maize.     

Dissection of the genetic architecture for grain quality‐related traits in three RIL populations of maize (Zea mays L.)

To manipulate the composition of the maize kernel to meet future needs, an understanding of the molecular regulation of kernel quality‐related traits is required. In this study, the quantitative trait loci (QTL) for the concentrations of grain protein, starch and oil were identified using three sets of RIL populations in three environments. The genetic maps and the initial QTL were integrated using meta‐analyses. A total of 38 QTL were identified, including 15 in population 1, 12 in population 2 and 11 in population 3. The individual effects ranged from 2.87% to 13.11% of the phenotypic variation, with seven QTL each contributing over 10%. One common QTL was found for the concentrations of grain protein and starch in bin 3.09 in the three environments and the three RIL populations. Of the 38 initial QTL, 22 were integrated into eight mQTL by meta‐analysis. mQTL3 and mQTL8 of the key mQTL in which the initial QTL displayed R² > 10% included six and three initial QTL for grain protein and starch concentrations from two or three populations, respectively. These results will provide useful information for marker‐assisted selection to improve the quality of the maize kernel.     

R-nj aleurone color selection and grain-filling responses in opaque-2 maize

Summary Field experiments were conducted to determine which grain-filling characteristics were affected by the o2 gene and whether mass selection for degree of aleurone anthocyanin pigmentation controlled by R-nj could improve the grain-fill deficiencies associated with the o2 (opaque) phenotype of a mazie (Zea mays L.) synthetic (NDSE). Divergent mass selection was used to develop high color (HC), low color (LC), and randomly sampled (RC) check substrains. Lag phase duration (LPD), effective filling period (EFPD), and rate of dry matter accumulation (RDMA) for both opaque and normal dent phenotypes of third cycle HC, LC, and RC substrains were evaluated at three N fertility levels for each of two years at Fargo. Normal (O2) pollen produced heavier kernels than o2 pollen at all N rates in 1982. Over years, O2 pollinations averaged 11% longer EFPDs than o2 pollinations, but LPDs were usually longer for o2 pollinations. HC strains averaged 5.6% higher RDMA than RC strains across pollen types while LC strains had higher RDMA than RC strains only for O2 pollinations. These results indicate that selection for LC improved several traits which were deficient in opaque-2 maize and that use of the R-nj gene may be useful in improving opaque-2 maize.Journal article No. 1756 of the North Dakota Agric. Exp. Stn., Fargo     

Genetic basis of variation for salt tolerance in maize ( Zea mays L).

The genetic basis of salt tolerance was examined in selected salt tolerant and sensitive material from a sample of accessions previously assessed for variability in salinity tolerance. The North Carolina Model 2 Design and analysis was followed, tolerance being assessed in 10-day-old seedlings grown in salinized solution culture at control (0 mM), 60 mM and 80 mM NaCl concentrations). Salinity tolerance was shown to be under the control of genes with additive and non-additive effects, with broad and narrow sense heritability estimates being approximately 0.7 and 0.4 over all treatments. This revised version was published online in July 2006 with corrections to the Cover Date.     

Development and mapping of gene-tagged SNP markers in laccases of maize (Zea mays L.)

Laccases, EC 1.10.3.2 or p -diphenol : dioxygen oxidoreductases, have been proposed to be involved in the oxidative polymerization of monolignols into lignins in plants. While 17 laccases have been identified in Arabidopsis , only five ( ZmLac1–5 ) have so far been identified in maize. By a bioinformatic approach, 14 putative laccases were identified in maize. One putative laccase was identical to ZmLac1 , while five were highly homologous to either ZmLac4 or ZmLac5 . Sequence alignment of allelic sequences enabled the development of TaqMan single nucleotide polymorphism (SNP) markers for nine putative laccases. Four of these gene-tagged SNP markers were validated in a doubled-haploid mapping population of 140 individuals, mapping these loci to chromosomes 1, 2, 3 and 7, respectively.     

Genetic mapping of quantitative trait locus for the leaf morphological traits in a recombinant inbred line population by ultra-high–density maps across multi-environments of maize (Zea mays)

Leaf is the main organ of photosynthetic reaction of plants. Studying the genetic mechanism that affects the leaf shape is very important for the improvement of maize production. In this study, a RIL population, derived from a cross between Ye478 and Qi319, was planted in four different environments, and six leaf morphological traits were measured, including the leaf angle of first leaf above ear, the leaf angle of first leaf below ear, leaf orientation value, leaf area of first leaf above ear, leaf area of ear and leaf area of first leaf below ear. By combining with a genetic map containing 4,602 bin markers, 39 QTLs associated with leaf morphological traits were identified. Among them, four QTLs explained more than 10% of the phenotypic variance, and the QTL qLOV8-2 which controlled LOV not only had a phenotypic contribution rate of 13.86% but also was detected in four environments, which could be considered as a stable major QTL. These results provide useful information for understanding the molecular mechanisms controlling maize leaf morphological traits.     

玉米籽粒突变体smk7的表型分析和基因定位

利用甲基磺酸乙酯(EMS)对玉米自交系B73进行诱变,获得一个可以稳定遗传的小籽粒突变体smk7(small kernel 7)。smk7成熟籽粒表现为体积变小,胚和胚乳发育缺陷,百粒重显著降低。突变籽粒发芽率仅为10%,且幼苗黄化不能生长成正常植株。成熟smk7胚乳中淀粉、蛋白、油分含量与野生型籽粒相比无显著差异,但突变体胚乳淀粉粒体积明显变小且形状不规则。smk7突变籽粒在授粉后12 d即可观察到明显的小籽粒和空瘪表型,石蜡切片显微观察显示突变籽粒的胚和胚乳发育迟缓,胚乳基部转移层细胞(BETL)相对于野生型细胞壁向内生长减少,发育受阻。用杂合植株(+/smk7)与多个自交系分别杂交,构建不同背景的F2分离群体,遗传分析结果表明该性状受单隐性核基因控制。利用靶向测序基因型分型(genotyping by target sequencing,GBTS)技术将基因初定位于2号染色体短臂,进一步精细定位发现该基因位于RM1433917和RM1535316两个标记之间约120 kb的物理范围内,共有8个蛋白编码基因。本研究为进一步克隆和解析SMK7基因调控玉米籽粒发育的分子机制奠定了基础。     

Variation among maize (Zea mays L.) accessions of Bendel State,Nigeria. Multivariate analysis of agronomic data

Summary Two multivariate techniques were used to characterize 30 maize accessions collected from three ecological zones of Bendel State, Nigeria. Differentiation of the 30 accessions into five distinct groups was achieved with the unweighted variable group method of the average linkage cluster analysis of 34 agronomic characters. Four of the taxonomic groups contained at least three accessions each, while a fifth group contained only one. The single accession contained in the fifth group was characterised by very early maturity, deeply pigmented leaves and ear husks and short statured plants. Clustering of the accessions into different phenetic groups followed substantially along geographical and traditionally trading routes. A few cases of overlapping of accessions from different geographical locations were obtained.Principal component analysis revealed that days to 50% tasseling and silking, number of nodes/plant, ear length, ear weight, leaf width, and kernel colour were the principal discriminatory characters that differentiated the accessions. Sixty-four percent of the total variation among the 34 characters were accounted for by the first five principal components while the first and second components accounted for 26 and 14 respectively.     

玉米籽粒突变体smk7的表型分析和基因定位

In this study, a stable small kernel mutant, named small kernel 7 (smk7), was isolated from ethylmethane sulfonate (EMS) mutagenesis of maize inbred line B73. Compared with wild type, the smk7 mutants showed smaller kernel size, defective embryo and endosperm development and a significant decrease in 100-kernel weight. The smk7 kernels showed a low level of germination rate at 10% and cannot grow into normal plants. No significant changes were detected in protein, starch and oil content between mature wild type and smk7 kernels, but the starch grains became significantly smaller and irregular in smk7 kernels compared with wild type. The smk7 kernels could be clearly distinguished from the wild type as early as 12 days after pollination (DAP), on the basis of their smaller and emptier phenotype. Microscopic inspection of the paraffin sections revealed that the development of embryo and endosperm were delayed, and the cell wall in growth in basal endosperm transfer layers (BETL) were arrested in smk7 compared with wild type. The F₂ populations with multiple backgrounds were constructed by crossing heterozygous plants (+/smk7) with several other inbred lines. Genetic analysis showed that the mutant phenotype was controlled by a single recessive gene. Based on genotyping by target sequencing (GBTS) strategy, the SMK7 was initially mapped on the short arm of chromosome 2. The fine mapping results suggested that SMK7 was located between markers RM1433917 and RM1535316, with a physical distance of 120 kb. There were eight protein-coding genes in this region. This study laid a foundation for further genes cloning and research of the SMK7 function in regulating maize kernel development.     

一个新的玉米Bt2基因突变体的遗传分析和分子鉴定

玉米籽粒发育调控机制的研究对于玉米产量与品质性状的遗传改良十分重要。本研究鉴定了一个新的转座子插入的籽粒皱缩突变体5601Q,遗传分析表明其籽粒缺陷稳定遗传且为单基因隐性突变。构建其B73背景的F2分离群体,通过图位克隆将该突变定位于玉米4号染色体上60.19～62.58Mb的区间。基因注释分析发现,区间内存在一个已报道参与玉米籽粒发育的基因BRITTLEENDOSPERM2(Bt2),其编码玉米胚乳淀粉合成途径中的一个限速酶——腺苷二磷酸葡萄糖焦磷酸化酶(ADP-glucose pyrophosphorylase, AGPase)的小亚基。籽粒储藏物质分析表明,该突变体百粒重及淀粉含量显著降低,但可溶性糖含量增加为野生型的4.67倍。利用本实验室已确定的Bt2基因突变体1774与5601Q进行等位测验,确认了5601Q是Bt2的一个新的等位突变体。分子鉴定表明,5601Q突变体中Bt2基因的第2个外显子存在一个Mutator 19转座子的插入。综上, 5601Q籽粒发育缺陷是由Bt2基因的突变导致,本研究为解析玉米Bt2基因在胚乳储藏物质积累中的作用机制提供了新的种质资源。     

Quantitative trait loci mapping for yield-related traits under low and high planting densities in maize (Zea mays)

Average maize yield per hectare has increased significantly because of the improvement in high-density tolerance, but little attention has been paid to the genetic mechanism of grain yield response to high planting density. Here, we used a population of 301 recombinant inbred lines (RILs) derived from the cross YE478 × 08–641 to detect quantitative trait loci (QTLs) for 16 yield-related traits under two planting densities (57,000 and 114,000 plants per ha) across four environments. These yield-related traits responded differently to high-density stress. A total of 110 QTLs were observed for these traits: 33 QTLs only under low planting density, 50 QTLs under high planting density and 27 QTLs across both densities. Only two major QTLs, qCD6 and qWKEL2-2, were identified across low- and high-density treatments. Seven environmentally stable QTLs were also observed containing qED6, qWKEL3, qRN3-3, qRN7-2, qRN9-2 and qRN10 across both densities, as well as qRN9-1 under low density. In addition, 16 and eight pairs of loci with epistasis interaction (EPI) were detected under low and high planting densities, respectively. Additionally, nine and 17 loci showed QTL × environment interaction (QEI) under low- and high-density conditions, respectively. These interactions are of lesser importance than the main QTL effects. We also observed 26 pleiotropic QTL clusters, and the hotspot region 3.08 concentrated nine QTLs, suggesting its great importance for maize yield. These findings suggested that multiple minor QTLs, loci with EPI and QEI, pleiotropy and the complex network of “crosstalk” among them for yield-related traits were greatly influenced by plant density, which increases our understanding of the genetic mechanism of yield-related traits for high-density tolerance.     

Genotype x environment interactions in a 10 × 10 diallel cross of quality protein maize (Zea mays L.)

Summary A 10×10 diallel cross experiment involving white modified opaque-2 maize inbred lines was grown at four sites. A stability analysis, based on both a combining ability and a heterotic pattern model, was developed. The stability analysis provided valuable information on the genotype x environment interaction properties of the 10 inbred lines. The Gail & Simon (1985) test for qualitative interactions provided a means of determining the nature of these interactions. The inbred, SO507W(M), is shown to have the best potential for use in a hybrid breeding programme, in terms of having the highest weighted general combining ability and line heterosis, and the best general adaptability to all four sites. The single cross, SO713W(P) x PO558W(F), has been identified as one of the genotypes to be used in a recurrent selection programme that favours specific combining ability.