Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

Genetic transformation has been an effective technology for improving the agronomic traits of maize.However,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype dependence.In this study,we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline(MQ2Gpipe).Based on the induction rate of EC(REC),these inbred lines were categorized into three subpopulations.The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.By integrating a genome-wide selective signature screen and region-based association analysis,we revealed 95.23 Mb of selective regions and 43 REC-associated variants.These variants had phenotypic variance explained values ranging between 21.46 and 49.46%.In total,103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci.These genes mainly participate in regulation of the cell cycle,regulation of cytokinesis,and other functions,among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction.Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci,implying a potential synergistic selection of REC and leaf size during modern maize breeding.

Genetic dissection of N use efficiency using maize inbred lines and testcrosses

Although the use of heterosis in maize breeding has increased crop productivity,the genetic causes underlying heterosis for nitrogen(N) use efficiency(NUE) have been insufficiently investigated.In this study,five N-response traits and five low-N-tolerance traits were investigated using two inbred line populations(ILs) consisting of recombinant inbred lines(RIL) and advanced backcross(ABL) populations,derived from crossing Ye478 with Wu312.Both populations were crossed with P178 to construct two testcross populations.IL populations,their testcross populations,and the midparent heterosis(MPH)for NUE were investigated.Kernel weight,kernel number,and kernel number per row were sensitive to N level and ILs showed higher N response than did the testcross populations.Based on a highdensity linkage map,138 quantitative trait loci(QTL) were mapped,each explaining 5.6%–38.8% of genetic variation.There were 52,34 and 52 QTL for IL populations,MPH,and testcross populations,respectively.The finding that 7.6% of QTL were common to the ILs and their testcross populations and that 11.7% were common to the MPH and testcross population indicated that heterosis for NUE traits was regulated by non-additive and non-dominant loci.A QTL on chromosome 5 explained 27% of genetic variation in all of the traits and Gln1-3 was identified as a candidate gene for this QTL.Genome-wide prediction of NUE traits in the testcross populations showed 14%–51% accuracy.Our results may be useful for clarifying the genetic basis of heterosis for NUE traits and the candidate gene may be used for genetic improvement of maize NUE.

Comparative Analysis of Genetic Diversity in Landraces of Waxy Maize from Yunnan and Guizhou Using SSR Markers

Waxy maize landraces are abundant inYunnan and Guizhou of China. Genetic diversity of waxy maize landraces from Yunnan and Guizhou were analyzed using SSR markers. We screened 38 landraces with 50 primers that generated 3 to 6 polymorphic bands, with an average of 4.13 bands. Shannon＇s information indices for genetic diversity of the 14 waxy maize landraces from Yunnan varied from 4.9571 to 42.1138 and averaged 26.5252; Shannon＇s information indices for genetic diversity of the 24 waxy maize landraces from Guizhou varied from 22.0066 to 40.6320 and averaged 32.3156. For the 14 waxy maize landraces from Yunnan, the within-landrace genetic diversity accounted for 45.40% and the among-landrace genetic diversity accounted for 54.60% of the total genetic diversity observed. For the 24 waxy maize landraces from Guizhou, the within-landrace genetic diversity accounted for 50.76% and the among-landrace genetic diversity accounted for 49.24% of the total observed. Some individual landraces possessed as much as 96.86% of the total genetic diversity occurring among landraces within origins. Differentiation between geographic origins accounted for only 3.14% of the total genetic diversity. Both Yunnan and Guizhou would be the diversity centers and the original centers of waxy maize.

Genetic Diversity of Maize Populations Developed by Two Kinds of Recurrent Selection Methods Investigated with SSR Markers

Two cycles of biparental mass selection （MS） and one cycle of half-sib-S3 family combining selection （HS-S3） for yield were carried out in 2 synthetic maize populations P4C0 and P5C0 synchronously. The genetic diversity of 8 maize populations, including both the basic populations and their developed populations, were evaluated by 30 SSR primers. On the 30 SSR loci, a total of 184 alleles had been detected in these populations. At each locus, the number of alleles varied from 2 to 14, with an average of 6.13. The number and ratio of polymorphic loci in both the basic populations were higher than those of their developed populations, respectively. There was nearly no difference after MS but decreased after HS-S3 in both the basic populations in the mean gene heterozygosity. The mean genetic distance changed slightly after MS but decreased in a bigger degree after HS-S3 in both the basic populations. Analyses on the distribution of genetic distances showed that the ranges of the genetic distance were wider after MS and most of the genetic distances in populations developed by HS-S3 were smaller than those in both the basic populations. The number of genotypes increased after MS but decreased after HS-S3 in both the basic populations. The genetic diversity of intra-population was much more than genetic diversity of inter-population in both the basic populations. All these indexes demonstrated that the genetic diversity of populations after MS was similar to their basic populations, and the genetic diversity was maintained during MS, whereas the genetic diversity of populations decreased after HS-S3. This result indicated that heterogeneity between some of the individuals in the developed populations increased after MS, whereas the populations become more homozygotic after HS-S3.

Genetic Diversity of Chinese Temperate and Exotic Tropical, Subtropical Quality Protein Maize Inbreds by SSR Markers

Information on genetic relationship is of great value to maize (Zea mays L.) breeding. Theobjectives of this study were: 1) to classify 22 quality protein maize (QPM) inbreds intodifferent groups by using simple sequence repeats (SSR) markers, which included exotictropical, subtropical and domestic temperate QPM and normal maize inbreds; 2) to examine theconsistency of grouping results obtained from SSR, specific combining ability (SCA) analysis,and genetic backgrounds of these inbreds. A set of 39 polymorphic SSR primers was selected from70 primer pairs, which detected 136 alleles among the 22 lines. The mean polymorphisminformation content was 0.55. Based on analysis of genetic similarities, five groups wereidentified including Luda Red Cob, Sipingtou, Reid, Lancaster and a miscellaneous group withseveral tropical inbreds which could not be classified into the above four groups. The resultsgenerally agreed with previous results based on analysis of yield combining ability andpedigree data.

Genetic Diversity of Two Important Groups of Maize Landraces with Same Name in China Revealed by M13 Tailed-Primer SSRs

Maize landraces White Dent and Golden Queen played a very important role in the pre-hybrid era of maize production in China. However, dozens of accessions with the same names of White Dent and Golden Queen are preserved in China National Genebank （CNG）. The present study investigated the genetic diversity of these two important groups of maize landraces, as well as the relationships within and among them. Thirty-four landrace accessions with the name of White Dent and 10 with Golden Queen preserved in CNG were fingerprinted with 52 simple sequence repeats with tailed primer M13. Summary statistics including average number of alleles per locus, gene diversity/expected heterozygosity, and observed heterozygosity were carried out using PowerMarker ver. 3.25 software. The test of Hardy-Weinberg equilibrium （HWE） and linkage disequilibrium （LD） of all the 44 maize landrace accessions were also performed by PowerMarker. We observed a significant differentiation in terms of the average number of alleles between White Dent and Golden Queen （6.44 alleles per locus in White Dent, 4.48 in Golden Queen）, while both groups of maize landraces had a relatively high but similar gene diversity （0.61 of White Dent, 0.63 of Golden Queen）. The fixation index （FST） was only 0.0044, while the percentage of loci deviated from Hardy-Weinberg equilibrium within these two groups of White Dent and Golden Queen was 32.69 and 3.92%, respectively. The rather high genetic diversity and average number of alleles per locus confirmed that both groups of landraces had a rather broad germplasm base. The extremely low fixation index showed that there was little genetic variation between White Dent and Golden Queen and the molecular variation within these two groups was remarkably high, indicating no genetic drift between White Dent and Golden Queen and suggesting different improvement approaches to these two important groups of landraces. Hardy-Weinberg equilibrium test revealed that the group of White Dent was deviated from HWE, whereas Golden Queen was under HWE.

QTL mapping of general combining abilities of four traits in maize using a high-density genetic map

General combining abilities （GCAs） are very important in utilization of heterosis in maize breeding. However, its genetic basis is unclear. In the present study, a set of 118 doubled haploid （DH） lines were induced from F1 generations produced from the cross between the inbred line Zheng 58 and the inbred line W499 belonging to the Reid subgroup. Using the MaizeSNP50 BeadChip, a high-density genetic map was constructed based on the DH population which included 1 147 bin markers with an average interval length of 2.00 cM. Meanwhile, the DH population was crossed with three testers including W16-5, HD568, and W556, which belong to the Sipingtou subgroup. The GCAs of the ear height （EH）, the kernel moisture content （KMC）, the kernel ratio （KR）, and the yield per plant （YPP） were estimated using these hybrids in three environments. Combining the high-density genetic map and the GCAs, a total of 14 QTLs were detected for the GCAs of the four traits. Especially, one pleiotropic QTL was identified on chromosome 1 between the SNP SYN16067 and the SNP PZE-101169244 which was simultaneously associated with the GCAs of the EH, the KR, and the YPP. These QTLs pave the way for further dissecting the genetic architecture underlying GCAs of the traits, and they may be used to enhance GCAs of inbred lines under the fixed heterotic pattern ReidxSipingtou in China through a marker-assisted selection approach.

Analysis of Genetic Diversity and Population Structure of Maize Landraces from the South Maize Region of China

Understanding genetic diversity and population structure of landraces is important in utilization of these germplasm in breeding programs. In the present study, a total of 143 core maize landraces from the South Maize Region （SR） of China, which can represent the general profile of the genetic diversity in the landraces germplasm of SR, were genotyped by 54 DNA microsatellite markers. Totally, 517 alleles （ranging from 4 to 22） were detected among these landraces, with an average of 9.57 alleles per locus. The total gene diversity of these core landraces was 0.61, suggesting a rather higher level of genetic diversity. Analysis of population structure based on Bayesian method obtained the samilar result as the phylogeny neighbor-joining （N J） method. The results indicated that the whole set of 143 core landraces could be clustered into two distinct groups. All landraces from Guangdong, Hainan, and 15 landraces from Jiangxi were clustered into group 1, while those from the other regions of SR formed the group 2. The results from the analysis of genetic diversity showed that both of groups possessed a similar gene diversity, but group 1 possessed relatively lower mean alleles per locus （6.63） and distinct alleles （91） than group 2 （7.94 and 110, respectively）. The relatively high richness of total alleles and distinct alleles preserved in the core landraces from SR suggested that all these germplasm could be useful resources in germplasm enhancement and maize breeding in China.

Study of Yield Combining Ability and Genetic Relationship Among Exotic Tropical,Subtropical Maize(Zea mays L.) Inbreds and Temperate Maize Inbreds in China

Information on the genetic relationship between tropical maize (Zea mays L), germplasm and temperate maize germplasm is of great value to maize breeding. The objective of this study was to determine the combining ability and genetic relationship of 25 inbreds extracted from five tropical maize populations and a land race, with four temperate maize inbreds (Huangzaosi, Mol7, B73 and Dan 340). The 25 tropical inbreds were crossed with the four temperate inbreds and evaluated. Lines from Suwanl and POP28 had high general combining ability (GCA) for grain yield. The lines from POP32 (ETO) had the highest special combining ability (SCA) with B73; the average SCA value of the 5 lines was 879 kg/ha. The lines from Suwanl had the second-highest SCA (584 kg/ha) with Huangzaosi. The lines from Suwanl had the greatest relative heterosis (20%) with B73, followed by the lines from POP32 (ETO) with B73 (19%). Five heterotic patterns have been identified from this study: Suwanl × Reid, ETO × Reid, POP28× Reid, POP28× Ludahong-gu, and Suwan1× Lancaster.

Genetic Analysis of the Resistance to Aspergillus flavus Infection in Maize (Zea mays L.)

Maize （Zea mays L.）, one of main crops in the world, is easily susceptible to Aspergillusflavus （Link： fr） infection, resulting huge loses worldwide. Breeding for A. flavus resistance has been proved an efficient way to solve the problem of aflatoxin contamination. Genetic analysis of the sources of resistance to A.flavus in maize is necessary for this purpose. The complete diallel crosses of 6 inbred lines with different resistance to A.flavus infection were implemented. Inoculation categorical data of each cross were analyzed with the additive-dominant and additive-dominant-epitasis genetic models. Results indicated some crosses fitted the 2 major genes with additive-dominant-epitasis genetic model. Others fitted the major gene and polygene mixed model. Moreover, the additive, dominant, and epitasis effects varied in crosses. The A.flavus resistance was controlled by both major gene and polygene.

A Comparative Analysis of B Chromosomes and Genetic Diversity in Maize (Zea mays L.) Landraces from Southwest China

The number of B chromosomes （Bs） in 54 maize landraces from Southwest China was tested by means of cytological observations. Nine landraces with Bs were observed. A map, showing the geographic distribution of the landraces with Bs, was plotted. It was found that southeastern Sichuan Province in China was the main distribution area of the landraces with Bs in Southwest China. In order to obtain information on relationships between Bs and genetic variation, genetic diversity both among and within 11 landraces was evaluated. For each SSR marker, the number of alleles ranged from 3 to 12 with an average of 7.86, which revealed a high level of genetic diversity among maize landraces in Southwest China. Based on SSRs data, higher genetic variation was found in the landraces with 2B, and the genetic distance between the landraces with and without Bs was higher. The results together with the principal component analysis （PCA） supported the hypothesis that maize landraces in Southwest China were first introduced to the middle part of southwest Sichuan, China. At the same time, the effect of Bs on genetic variation was discussed.

Genomic prediction of yield performance among single-cross maize hybrids using a partial diallel cross design

Genomic prediction(GP)in plant breeding has the potential to predict and identify the best-performing hybrids based on the genotypes of their parental lines.In a GP experiment,34 elite inbred lines were selected to make 285 single-cross hybrids in a partial-diallel cross design.These lines represented a mini-core collection of Chinese maize germplasm and comprised 18 inbred lines from the Stiff Stalk heterotic group and 16 inbred lines from the Non-Stiff Stalk heterotic group.The parents were genotyped by sequencing and the 285 hybrids were phenotyped for nine yield and yield-related traits at two locations in the summer sowing area(SUS)and three locations in the spring sowing area(SPS)in the main maizeproducing regions of China.Multiple GP models were employed to assess the accuracy of trait prediction in the hybrids.By ten-fold cross-validation,the prediction accuracies of yield performance of the hybrids estimated by the genomic best linear unbiased prediction(GBLUP)model in SUS and SPS were 0.51 and 0.46,respectively.The prediction accuracies of the remaining yield-related traits estimated with GBLUP ranged from 0.49 to 0.86 and from 0.53 to 0.89 in SUS and SPS,respectively.When additive,dominance,epistasis effects,genotype-by-environment interaction,and multi-trait effects were incorporated into the prediction model,the prediction accuracy of hybrid yield performance was improved.The ratio of training to testing population and size of training population optimal for yield prediction were determined.Multiple prediction models can improve prediction accuracy in hybrid breeding.

Determination of the Number of SSR Alleles Necessary for the Analysis of Genetic Relationships Between Maize Inbred Lines

The amount of molecular marker information has considerable impact on the results of studies of crop germplasm genetic relationships in crop. The number of alleles required to reveal genetic relationship in maize inbred lines is a theoretical issue that needs to be addressed. In this study, 112 pairs of SSR （simple sequence repeat） primers and 97 maize inbred lines were selected to study the relationship between the number of inbred lines and the number of SSR primers and alleles required for a stable cluster. The results showed that the number of SSR primers is not tightly associated with the stability of the cluster analysis results, while an increase in the number of alleles can significantly improve the stability of cluster analysis results. The number of inbred lines （X） is significantly associated with the number of alleles required for stable cluster analysis （Y）, and the regression equation is Y- 600.8xe（-15.9/x）. This equation can be used to calculate the number of SSR alleles required for a genetic relationship study of maize inbred lines. These results provide a reference for determining of SSR alleles number in genetic relationship analysis of maize inbred line and other crop germplasm.

Genetic analysis of maturity and flowering characteristics in maize(Zea mays L.)

Objective:To elucidate the pattern of inheritance and determine the relative magnitude of various genetic effects for maturity and flowering attributes in subtropical maize.Methods: Four white grain maize inbred lines from flint group of corn,two with late maturity and two with early maturity,were used.These contrasting inbred lines were crossed to form four crosses.Six generations(P_1,P_2,F_1,F_2,BC_1,and BC_2) were developed for each individual cross.These were evaluated in triplicate trial for two consecutive years.Results:Roth dominance gene action and epistatic interaction played major role in governing inheritance of days to pollen shedding, 50%silking,anlbesis silking interval and maturity.Conclusions:Preponderance of dominance gene action for these traits indicated their usefulness in hybrid programs of subtropical maize.

Genetic Relationships Among Chinese Maize OPVs Based on SSR Markers

Bulk-SSR method was used to analyze the genetic diversity of 44 open-pollinated varieties collected from Henan, Shandong, Shanxi, and Jilin provinces and Guangxi Zhuang Autonomous Region, China using 70 pairs of SSR primers. The purposes of this study were to （1） compare the genetic diversity among 44 Chinese maize open-pollinated varieties; （2） estimate the minimum number of alleles for construction of a stable dendrogram; and （3） trace the genetic relationships among local germplasm from different regions of China. In total, these 70 SSR primers yielded 292 alleles in 176 samples （4×44） analyzed. The number of alleles per locus was 4.17 on average and ranged from 2 to 8. The highest number of alleles per open-pollinated variety （55.25） was detected in Shanxi germplasm, which indicated that open-pollinated varieties from Shanxi possessed the largest genetic diversity among those from the five locations. The correlation coefficients between different genetic similarity matrices suggested that 200 alleles were sufficient for analysis of the genetic diversity of these 44 open-pollinated varieties. The cluster analysis showed that 44 open-pollinated varieties collected from three growing regions in China were accurately classified into three groups that were highly consistent with their geographic origins, and there is no correlation between GS and geographic distance in this study.

An Analysis on the Relationship between Maize Heterosis and Genetic Distance

13 normal maize inbred lines with quite different quantitative traits were used as experimental materials in this paper. The results showed that there was significantly positive correlation between genetic distance and plot yield,mid-parent heterosis,super heterosis,or SCA of yield. In a certain range,the longer the genetic distance between parental inbred lines,the stronger the heterosis. Therefore,in genetic practice,it was necessary to take the molecular genetic distance between inbred lines as an important reference.

Phylogenetic Analysis among Maize Exserohilum turcicum Isolates from Yunnan Province by RAPD

[ Objective ] This study aimed to investigate the genetic variation of Yunnan Exserohilum turcicum isolates from molecular level, and provide theoretical basis for E. turcicum pathogenicity virulence differentiation and effective control of disease. [Method] A total of 56 E. turc/cum isolates from some areas of Yunnan Province were analyzed by RAPD. Based on the genetic distance, a dendrogram was constructed. [Result] Ten genetic groups were formed in the dendrogram. The RAPD groups had no obvious correlation with geographic origins. Some strains from one area were closely related to some from another area. [ Conclusion] Rich ge- netic variation existed among the tested isolates.

Genetic Diversity for Yield and Yield Contributing Characters of Short Statured Maize Inbred Lines

Genetic diversity is one of the useful tools to select appropriate lines for hybridization. Twenty short-statured maize inbred lines were taken for present study, which were collected from CIMMYT India and Mexico through Plant Breeding Division, Bangladesh Agricultural Research Institute (BARI), Gazipur. This experiment was conducted from November 2015 to April 2016 to identify parental lines to produce single cross short statured maize hybrids. From the genetic diversity studies, the importance of both additive and non-additive gene actions for the expression of yield and yield contributing characters were found. Values of vector I and II revealed that both the vectors had positive values for date of silking, plant height, rows/cob, grains/row and yield. These results indicated that these five characters had highest contribution towards divergence. Based on the relative magnitude of D2 values;20 inbred lines were grouped into five clusters. Seven inbred lines were selected on the basis of genetic diversity and per se performance which will be crossed separately in a half-diallel fashion to develop hybrids.

Genetic Diversity and Genetic Structure of Maize Inbred Lines from Yunnan Revealed by SNP Chips

[Objectives]The genetic diversity and population genetic structure of 107 inbred lines of maize in Yunnan were analyzed,in order to provide technical support for maize germplasm innovation,genetic improvement of germplasm resources,variety management,and lay a solid foundation for exploring genes related to fine traits in the future.[Methods]The 107 maize inbred lines generalized in Yunnan were selected,and 45 backbone inbred lines commonly used in China were used as reference for heterotic group classification.On Axiom Maize 56K SNP Array platform,maize SNP chips(56K)were used to scan the whole maize genome,and the NJ-tree model of Treebest was used to construct a phylogenetic tree.Principal component analysis(PCA)was conducted by GCTA(genome-wide complex trait analysis)to reveal the genetic diversity and population genetic structure.[Results]In the 107 Yunnan local inbred lines,5533 uniformly distributed high-quality SNP marker sites were finally detected.Based on the analysis of these SNP marker sites,Nei s gene diversity index(H)of 107 maize germplasm genes was 0.2981-0.5000 with an average value being 0.4832,and polymorphism information content(PIC)values were 0.2536-0.3750 with an average value being 0.3662.The minimum allele frequency value was 0.5000-0.8178 with an average value being 0.5744.The analysis of population genetic structure showed that when K=6,the maximum value of△K was the maximum,which meant that the inbred lines used in this study could be divided into six groups.They were Tangsi Pingtou blood relationship group,PB blood relationship group,335 female blood relationship group,Zi 330 and the Lüda Honggu blood relationship group,unknown group 1 and unknown group 2.No inbred lines were divided into other heterotic groups.Among them,37 inbred lines from the 2 unknown groups could not be classified into the same group as the 10 known heterotic groups in China.The results of principal component analysis showed that the 107 maize inbred lines generalized in Yunnan could be clearly distinguished from the backbone maize inbred lines commonly used in China.Most of the maize inbred lines in Yunnan were concentrated near the reference backbone inbred lines.But some Yunnan inbred lines were far away from the reference inbred lines commonly used in China.[Conclusions]The maize germplasm resources in Yunnan area were rich in genetic diversity,including multiple heterotic groups,and there was a rich genetic basis of breeding parents.They could be clearly distinguished from the backbone inbred lines commonly used in China,and some of them had a long genetic distance from the backbone inbred lines.The resources which have good application potential can be used to create new heterotic groups.

Genetic Analyses of Tolerance to Low Nitrogen in Tropical Maize Germplasm

Six tropical maize inbred lines were crossed in a half diallel fashion and evaluated along with their F1 hybrids under low N (0 kg/ha) and high N(170 kg/ha), for grain yield, ear diameter, ear length, number of rows per ear, 100-kernel weight, ear leaf area, shoot dry weight, ear leaf chlorophyll content and plant height to determine their response to different level of N. Grain yield and ear leaf chlorophyll content measured by 48% lower under -N than under + N, and were most affected by -N. Ear length had the highest reduction under -N of 22%. Plant height and shoot dry weight were both reduced by 28%. Diallel analysis indicated significant additive as well as dominance variance for grain yield under -N. The same results were shown when one tolerant x nontolerant cross from the diallel hybrids was subjected to generation mean analysis which also indicated significant epistatic effects. These results suggest that S1 or S2 progeny selection may be an effective means of improving grain yield of tropical maize under low soil N.