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玉米自交系遗传变异的RFLP分析


植        物 学 报 2000 , 42 (11) :1156 - 1161
Acta Botanica Sinica

 

 

 

 

 

 

 

玉米自交系遗传变异的 RFLP 分析

r />李新海   傅骏骅   张世煌   袁力行   李明顺
( 中国农业科学院作物育种栽培研究所 ,农业部作物遗传育种重点开放实验室 , 北京 100081)

摘要 :   利用 RFLP 标记研究了 13 个玉米 ( Zea mays L. ) 自交系的遗传变异 。从 30 对探针/ 酶组合中筛选出杂交带 型清晰 、 稳定 、 重复性好的 24 对组合 ,在 13 个自交系中获得 85 个等位基因杂交片段 ,平均每个位点为 3. 3 条 ,平均 多态性指数为 0. 499 。13 个自交系之间的遗传相似系数为 0. 523~0. 802 ,平均为 0. 649 。UPG 聚类分析表明 ,供 MA 试自交系共分为 5 个类群 ,分群结果与其系谱关系基本吻合 ; 表明利用 RFLP 标记可以研究玉米自交系之间的遗传 关系 ,并将无系谱记载的自交系划分到相应类群中 。 关键词 :   玉米 ; RFLP 标记 ; 遗传相似系数 ; 杂种优势群 中图分类号 : S513. 032     文献标识码 : A     文章编号 : 057727496 (2000) 1121156206 ? 1995-2004 Tsinghua Tongfang Optical Disc Co., Ltd. All rights reserved.

RFLP Detection of Genetic Variation of Maize Inbred Lines
LI Xin- Hai , FU J un- Hua , ZHANG Shi- Huang , Y UAN Li- Xing , LI Ming- Shun
( Institute of Crop Breeding and Cultivation , Chinese Academy of Agricultural Sciences ;
Key Laboratory of Crop Genetics and Breeding , Ministry of Agriculture , Beijing 100081 , China)

Ξ

  Utilization of heterosis is the most efficient approach to improve maize performance. Abundant heterosis is manifested from the cross of two genetically diverse in2 breds , and inbreds derived from certain unrelated or dis2 tantly related groups of maize materials combine well and develop good hybrids through outstanding performance. Thus knowledge of genetic relationships among inbred lines is essential to maize breeders for exploitation of het2 erosis. Accordingly , maize inbreds with unknown pedi2 gree and heterotic response should be assigned to known heterotic groups to facilitate hybrid and inbred line devel2 opment . Genetic relationships can be estimated based on
Received : 2000201231   Accepted : 2000203231 Foundation item : The Asian Maize Biotechnology Network Project .

Abstract :  Genetic similarities of 13 inbred lines of maize ( Zea mays L. ) were analyzed by restriction frag2 ment length polymorphisms ( RFLPs) . The objectives of the study were to detect genetic similarities among 13 inbreds and to assign them to heterotic groups. By means of 24 probe-enzyme combinations ( PECs) selected for locus specificity , clear patterns and reproducibility , 85 alleles were found with an average of 3. 3 alleles per locus. The allelic frequency data were used to estimate genetic similarities among lines , and as a result the di2 versity index of 0. 499 was obtained. Genetic similarities between the pairs of 13 lines ranged from 0. 523 up to 0. 802 with an average of 0. 649. The UPG MA clustering algorithm analysis classified the 13 lines into five groups , which generally corresponded to known maize heterotic groups based on pedigree information. The au2 thors concluded that RFLP- based markers could be used for investigating genetic relationships between maize inbred lines and assigning them to heterotic groups , but it seemed that a large number of PECs were needed to obtain reliable estimates of genetic similarity. Key words :  Zea mays ; restriction fragment length polymorphisms ( RFLPs) ; genetic similarity ( GS) ; het2 erotic group

Ξ

pedigree data , morphological traits , or molecular markers such as isozymes , RFLPs or PCR- based markers. The Malecot ’ coancestry coefficient [1 ] is a measure of genetic s diversity , which is widely used to estimate levels of genet2 ic relationships between two cultivars in wheat [2 ] and soy2 bean [3 ] . For maize , the coefficient has not been easily determined because of unobtainable or unreliable pedi2 gree. Morphological traits have been traditionally used in plant variety protection and registration for description of identity and distinctions of cultivars and inbreds. Howev2 er , the evaluations of morphological characters require ex2 tensive observation of mature plants , and in many cases they lack definition and objectivity due to environmental

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李新海等 : 玉米自交系遗传变异的 RFLP 分析 ( 英)

 

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factors[4 ] . Biochemical data provide superior descriptions of the genotype because they are not significantly affected by environments. Isozymes have been used extensively to characterize genetic variation among inbred lines of maize [5 ] . However the major limitation of the biochemical assays is the insufficient polymorphic loci detected. As isozymes are the products of gene expression , they may vary in different tissues and developmental stages[6 ] . Re2 cent advances in techniques for DNA analysis have result2 ed in alternative DNA- based procedures for the detection of polymorphism. The most widely used approach is re2 striction fragment length polymorphism ( RFLP) analysis. A number of studies in maize indicated that RFLPs could be used to investigate pedigree relationships among in2 breds and to assign them to heterotic groups[7 - 10 ] . No attempts have been reported to detect genetic similarity by RFLP markers among maize inbred lines in China. The objectives of this study were to detect genetic similarity among 13 maize inbred lines , and to assign them to known heterotic groups. It was specially focused on the choice of parental lines for mapping genetic loci re2 sponsible for resistance to sugarcane mosaic virus ( SCMV) and drought tolerance , respectively.

1  Materials and Methods

1. 1  Plant materials A sample of 13 maize ( Zea mays L. ) inbred lines ( Table 1) consisted of widely used inbred lines in maize hybrid breeding programs in China was used for detecting the genetic similarity by RFLPs in the study. Four of these lines were selected , as they were either resistant or susceptible lines to SCMV. Three lines have been used as drought tolerant ones in breeding programs. Both Qi 205
Table 1   Description of 13 maize inbred lines and their pedigree
No. 1 2 3 4 5 6 7 8 9 Inbred line Pedigree Huangzao 4

Tangsipingtou open pollination

Pa405

Mo17 5003

C103 × 187-2

PN germplasm PN germplasm

Zhongzi 451 Han 23 Hai 9-21 Ye 478 K12

Dan 340 CA375

Baigulu 9 × Podcorn 5003 × 8112 Pool33

10 11 12

Huangzao 4- derived line

Qi 205

(Vai141 × CAo17) × . 70 Pop

13 Wu 105 SCMV , sugarcane mosaic virus ; QPM , quality protein maize.

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and CA375 were important quality protein maize ( QPM) lines in China. Four typical lines were included to repre2 sent known heterotic groups. They were Mo17 of Lancast2 er Sure Crop (LSC) , Huangzao 4 of Tangsipingtou , Dan 340 of Luda Red Cob , and Ye 478 of PN groups. The lines were maintained by selfing from seed of individual ears. 1. 2   Laboratory analysis Equal quantities of young leaf tissue ( 5 - 6 weeks old) harvested in bulk from fifteen seedlings of each line were lyophilized and ground to fine powder with a me2 chanic mill . Genomic DNA was extracted according to Saghai-Maroof et al [11 ] , quantified by the Beckman DU65 spectrophotometer and digested with Eco R Ⅰ or Hin d Ⅲ Digested DNA samples ( 10 μ ) were loaded . g onto 0. 8 % agarose gels subjected to overnight elec2 trophoresis ( 16 - 18 h) in 1 ×TAE ( 40 mmol/ L Tris , 5 mmol/ L NaOAc , 0. 77 mmol/ L EDTA) . Filters were hy2 bridized with digoxigenin- dUTP labeled probes overnight at 65 ℃in hybridization buffer ( 3. 7 mol/ L NaCl , 0. 375 mol/ L Na- Citrate , pH 7. 4 , 0. 01 % laurylsarcosine , 0. 02 % SDS , 0. 2 % Blocking reagent) buffer. After hy2 bridization , 0. 1 × SSC and 0. 1 % SDS were used to wash membranes in a tank for 3 - 5 min at 90 - 93 ℃ T ac2 . o count for possible migration distortions , a set of molecular weight markers of 24 kb (obtained from Xba Ⅰ restriction of λ DNA) , and 1. 5 kb were added to each DNA samples just before loading the gels. λ DNA/ Hin d Ⅲ fragments (23. 1 , 9. 4 , 6. 5 , 4. 4 , 2. 3 , and 2. 2 kb) were also run in one lane per comb. A subset of 15 genomic probes was used as RFLP probes in the study. These probes were selected for their single or double banding patterns provided among a total
Annotation Tangsipingtou group , SCMV resistant SCMV resistant Lancaster Sure Crop group , SCMV susceptible SCMV susceptible SCMV susceptible Drought tolerant Drought tolerant Luda Red Cob group QPM line QPM line PN group , SCMV susceptible SCMV resistant Drought tolerant

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of 42 probes in combination with Eco R Ⅰ and Hin d Ⅲ . Fifteen probes and their chromosomal locations are given in Table 2. Probes revealing more than one locus were discarded to detect genetic polymorphism because of the complexity of banding patterns. 1. 3   Statistical analysis Pair-wise comparisons of genotypes for RFLPs were made based on both unique and shared fragments. Genet2 ic similarities ( GS ) were estimated from the allele fre2 quency data using a simple matching coefficient , i . e. GS = m/ ( m + n ) , where m is the number of matches and n is the number of mismatches. Associations among 13 inbreds were determined based on the matrix of GS by Unweighted Pair Group Method using Arithmetic Average (UPG ) clustering analysis performed with the program MA NTSYS- PC version 1. 8 [12 ] . The average number of alleles per locus was calculated over the entire set of lines for all the probe-enzyme combinations ( PECs) . A Nei ’ diversi2 s [13 ] ty index was estimated for each PEC as follows : Hi = 1 - Σ P2ij , where Pij is the frequency of the jth profile with the i th PEC.

2  Results and Discussion

2. 1  RFLP profiles Twenty-two out of 30 PECs resulted in RFLP pat2 terns with a single band per line ( Fig. 1) , two gave dou2 ble patterns ( umc17 combined with both restriction en2 zyme digests) , while six gave multiple- banded RFLP pat2 terns , suggesting the presence of sequence repetition in the genome ( data not shown) . All the 24 PECs ( Table 2 ) revealed polymorphism among the 13 inbreds , and produced a total of 85 alleles. The average number of al2 leles per locus was 3. 3. This value was lower than the polymorphism of 5. 8 obtained by Livini et al [14 ] among

Fig. 1.   RFLP profile of 13 maize inbred lines hybridized by umc21/ EcoR Ⅰ. M ,λ DNA/ Hind Ⅲ molecular weight standard ; 1 - 13 , 13 inbred lines ( The number is the same as in Table 1) ; CK, black control.

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40 U. S. dent lines for 70 genomic probes and of 5. 9 found by Dubreuil et al [15 ] among 116 lines for 63 PECs. However , Messmer et al [5 ] reported a mean polymor2 phism , lower than 4 alleles per locus among 30 early ma2 turing inbred lines. In the present study the use of singlecopy probes and fewer lines could account for the lower level of polymorphism detected. Twenty-four PECs produced two to seven different RFLP variants across the 13 inbred lines. A unique RFLP profile for each inbred line could be obtained from these variants , even for highly related lines ( such as Ye 478 and 5003 with a coancestry coefficient of f = 0. 5 ) dif2 fered in their RFLP pattern in 17 alleles. This confirms that RFLP marker is a powerful tool in determining genet2 ic relationships among maize inbred lines.    average diversity index of 0. 499 among 13 in2 An bred lines ranging from 0. 278 for umc34/ Eco R Ⅰ to 0. 792 for bnl13. 05/ Hin d Ⅲ was found. Among the 85 alleles , 58. 8 % of the alleles occurred at a frequency of 0. 1 or less , while only 8. 2 % of the alleles occurred at a frequency of 0. 5 or greater. The high diversity was main2 ly due to the lower level of gene frequency at each of the allelic loci . Dubreuil et al [15 ] reported that 52. 4 % of the 372 RFLPs within 116 maize inbred lines had a frequency lower than 0. 1 whereas only 8. 1 % had a frequency high2 er than 0. 5. Similarly , they contributed this high diversi2 ty index to numerous alleles present in low frequency. Compared with previous studies of the allozyme variability among inbreds , the diversity index of RFLPs obtained in this study was higher. Cardy and Kannenberg[16 ] observed that 35. 3 % of the alleles at 18 polymorphic enzyme loci occurred at a frequency higher than 0. 5 within 10 inbreds from North American and Canadian germplasm. By

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Table 2   Description of the 24 probe- enzyme combinations assayed in 13 inbred lines of maize
  Probe
umc128 umc6 umc34 umc131 umc17 umc66 umc27 bnl5. 71 umc21 umc80 bnl13. 05 umc30 umc81 bnl14. 28 bnl7. 49 T otal Chromosome 1 2 2 2 3 4 5 5 6 7 8 8 9 9 10 Map position (cM) 1) 168. 1 50. 6 70. 2 90. 4 117. 5 101. 9 56. 9 101. 1 87. 6 114. 4 10. 5 112. 5 72. 5 117. 3 147. 5 Enzyme
EcoR Ⅰ Hind Ⅲ EcoR Ⅰ Hind Ⅲ EcoR Ⅰ Hind Ⅲ Hind Ⅲ EcoR Ⅰ Hind Ⅲ Hind Ⅲ EcoR Ⅰ Hind Ⅲ EcoR Ⅰ Hind Ⅲ EcoR Ⅰ Hind Ⅲ Hind Ⅲ Hind Ⅲ EcoR Ⅰ Hind Ⅲ EcoR Ⅰ Hind Ⅲ Hind Ⅲ Hind Ⅲ

N12) 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

N23) 4 2 3 2 2 3 2 6 4 3 2 3 5 4 4 3 4 5 4 4 3 3 7 4 85

Hi

0. 535 0. 375 0. 429 0. 397 0. 278 0. 604 0. 486 0. 237 0. 347 0. 542 0. 375 0. 591 0. 757 0. 471 0. 625 0. 569 0. 625 0. 792 0. 719 0. 695 0. 486 0. 625 0. 764 0. 417 12. 978 0. 499

Mean 3. 3 1) Map distance was determined from the 1998 UMC Maize Map ; 2) N1 , number of loci involved ; 3) N2 , number of alleles detected.

comparing Atlantic Cod populations for allozyme polymor2 phism and nuclear RFLP , Pogson et al found a significant discrepancy for allelic frequency patterns between isozymes and RFLPs[17 ] . The fact could account for this discrepancy that only mutations within exons can induce a shift in the protein charge , while most point mutations do not modify the global charge of proteins , but such muta2 tions can be detected by RFLPs[15 ] . This suggests that the difference between RFLPs and allozyme variation may be affected by the reproductive system. 2. 2  Genetic similarities ( GS ) among 13 inbred lines GS values among the pairs of 13 inbred lines are given in Table 3. GS values across all 78 pairs of 13 lines averaged 0. 649 , ranging from 0. 523 between Huangzao 4 vs. 5003 up to 0. 802 between 5003 vs. Ye 478. As Huangzao 4 was SCMV resistant line and 5003 susceptible line , the lowest GS suggested that both lines could be used as parents to make cross for mapping SCMV resistant gene. The largest GS value between Ye 478 and 5003 was mainly due to Ye 478 , which originated from a cross between 5003 × 8112. GS estimates for the combinations of Huangzao 4 ×Mo17 , Huangzao 4 × Ye 478 , and Huangzao 4 × Dan 340 were 0. 581 , 0. 581 and 0. 627 , respectively. This suggested that Huangzao 4 possessed a

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larger genetic distance with two exotic lines ( LSC and PN) than the domestic line (Luda Red Cob group ) . The combinations of Dan 340 × Mo17 and Dan 340 ×Ye 478 were 0. 697 and 0. 581 in genetic similarities , respective2 ly. The GSs for drought tolerant line combinations of Hai 9-21 ×Han 23 , Hai 9-21 × Wu 105 and Han 23 × Wu 105 were 0. 728 , 0. 592 and 0. 593 , respectively , suggesting that Wu 105 had a similar genetic distance to each of Han 23 and Hai 9-21 , and the latter two lines were very closely related. Qi 205 and CA375 possessed a higher GS value of 0. 682 than the average GS of 0. 649. This result was inconsistent with breeding empirical that Qi 205 and CA375 were good combiners and presumed a large genetic distance , as the cross between these two lines was an elite commercial hybrid with good perfor2 mance. It could be accounted for this discrepancy that limited PECs were used in the study and the genetic loci provided by PECs used may be incorrelated with the loci controlling the yield heterosis between Qi 205 and CA375. 2. 3   Cluster analysis of RFLP data The UPG MA clustering method classified the 13 lines into four major groups designated A through D ( Fig. 2) . Cluster A consisted of two subgroups ( A′ A″. and ) Qi 205 and Mo17 grouped before joining with Wu 105 to

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Table 3  Genetic similarities between 13 inbred lines of maize based on 85 RFLP variants
Qi 205 K12 CA375 Ye 478 Dan 340 Hai 9-21 Han 23 Zhongzi 451 5003 Mo17 Pa405 Huangzao 4 Wu 105 0. 697 0. 682 0. 627 0. 604 0. 592 0. 709 0. 697 0. 709 0. 790 0. 604 0. 627 0. 767 0. 609 0. 627 0. 651 0. 567 0. 593 0. 744 0. 639 0. 651 0. 651 0. 720 0. 651 0. 585 0. 609 0. 597 0. 573 0. 658 0. 524 0. 609 0. 658 0. 609 0. 658 0. 581 0. 641 0. 639 0. 651 0. 802 0. 697 0. 674 0. 581 0. 651 0. 667 0. 686 0. 720 0. 616 0. 697 0. 674 0. 627 0. 627 0. 728 0. 617 0. 580 0. 592 0. 567 0. 691 0. 592 0. 662 0. 767 0. 755 0. 569 0. 593 0. 593 0. 709 0. 720 0. 651 0. 651 0. 581 0. 689 0. 686 0. 523 0. 686 0. 674 0. 581 0. 744 0. 534 0. 604 0. 674 K12 CA375 Ye 478 Dan 340 Hai 9-21 Han 23 Zhongzi 451 5003 Mo17 Pa405 Huangzao 4

comprise subgroup A′ Subgroup A″contained two PN . lines of Ye 478 and 5003. Huangzao 4 and its derivative K12 were found in group B. Two drought tolerant lines of Han 23 and Hai 9-21 and Dan 340 clustered to group C. Group D contained one SCMV resistant line Pa405 and one QPM line CA375.    Grouping of inbreds revealed by the UPG analy2 MA sis was generally in agreement with the pedigree of these lines and the clusters were representatives of heterotic groups. Mo17 , Ye 478 , Huangzao 4 and Dan 340 were the typical lines of LSC , PN , Tangsipingtou and Luda Red Cob groups , respectively. Several elite single crosses have been developed between these four lines , and were widely used in maize production in China. Our RFLPs clearly differentiated these lines from one another , and placed them in separate groups. Ye 478 was developed from the cross of 5003 × 8112. The RFLPs revealed that the highest genetic similarity was found with Ye 478 and its relative 5003 at the molecular level , as also shown by the adjacent placement of both lines in UPG MA clusters. Qi 205 was a cross between Vai141 and CAo17 , which was then crossed to population 70. CAo17 was a conver2 sion line of Mo17 under opaque-2 background. The high GS value between Qi 205 and Mo17 was consistent with their pedigree information. Although Pa405 , an exotic

Fig. 2.   Clusters of 13 inbred lines of maize based on RFLP mark 2 ers.

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line resistant to SCMV , grouped with CA375 developed from Pool 33 composted by subtropical maize germplasm , there existed considerable low GS between the two lines. One discrepancy was present , i . e. , the grouping of K12 and Zhongzi 451 in group B. Zhongzi 451 was developed from PN germplasm , which contained some Reid Yellow Dent germplasm , whereas K12 was a related line of Tangsipingtou group . Such incongruity is common when comparing the results of molecular analysis with classifica2 tions based on pedigree. By comparison , incongruity may be explained by several factors[18 ] . DNA markers , when identical in size , may represent alleles that are only iden2 tical in state , and may not always be identical by de2 scent . A combination of selection , random drift and mu2 tation can also be responsible for reducing the correlation between the two measures of similarity. In addition , in2 congruity can result from the clustering process in which an inbred line that is related to two other inbred lines from separate clusters will only be grouped with the one to which it is most closely related. Finally , it seemed that more polymorphic loci were needed to obtain reliable esti2 mates of genetic similarities between the 13 maize inbred lines tested in the study. Whenever happened , our results supported that RFLP- based genetic similarity estimates could investigate relationships between these inbred lines and assign them to established heterotic groups. References :

[1 ]  Malecot G. Les Mathematiques de I’ Heredite. Paris : Maa2 son et Cie , 1948. [2 ]  Cox T S , Lockhart GL , Walker D W , Harrel L G, Albers L D , Rodgers D M. Genetic relationships among hard red winter wheat cultivars as evaluated by pedigree analysis and gliadin polyacrylamide gel electrophoresis patterns. Crop Sci , 1985 , 25 :1058 - 1063. [3 ]  Cox T S , K iang Y T , G orman M B , Rodgers D M. Rela2 tionship between coefficient of parentage and genetic similar2 ity indices in the soybean. Crop Sci , 1985 , 25 :529 - 532.

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[ 4 ]  Yang X , Ouiros C. Identification and classification of celery cultivars with RAPD markers. Theor Appl Genet , 1993 , 86 : 205 - 212. [5 ]  Messmer M M , Melchinger A E , Lee M , Woodman W L , Lee E A , Lamkey K R. Genetic diversity among progenitors and elite lines from the Iowa Stiff Stalk Synthetic ( BSSS) maize population : Comparison of allozyme and RFLP data. Theor Appl Genet , 1991 , 83 :97 - 107. [6 ]  Beckman J S , Soller M. Restriction fragment length poly 2 morphisms in genetic improvement : Methodologies , mapping and costs. Theor Appl Genet , 1983 ,67 :35 - 43. [7 ]  Dudely J W , Saghai-Maroof M A. Molecular marker and grouping of parents in maize breeding programs. Crop Sci , 1991 , 31 :718 - 723. [ 8 ]  G odshalk E B , Lee M , Lamkey K R. Relationship of re2 striction fragment length polymorphisms to single cross hy 2 brid performance of maize. Theor Appl Genet , 1990 , 80 : 273 - 280. [ 9 ]   M, G Lee odshalk E B , Lamkey K R , Woodman W W. As 2 sociation of restriction fragment length polymorphisms among maize inbreds with the agronomic performance of their cross 2 es. Crop Sci , 1989 , 29 :1067 - 1071. [10 ]   Smith J S C , Smith O S. Restriction fragment length poly 2 morphisms can differentiate among U. S. maize hybrids. Crop Sci , 1991 , 31 :893 - 899. [11 ]   Saghai-Maroof M A , Soliman K M , Jorgenson R , Allard R W. Ribosomal DNA spacer length polymorphisms in barley :

Mendelian inheritance , chromosome location and population dynamics. Proc Natl Acad Sci USA , 1984 , 81 : 8014 8018. [12 ]  Rolf J F. NTSYS-pc : Numerical taxonomy and multivariate analysis system. Version 1. 8. Exeter Software Setauket , New Y , 1992. ork [13 ]   M. Analysis of gene diversity in subdivided populations. Nei Proc Natl Acad Sci USA , 1973 , 70 :3321 - 3323. [14 ]   Livini C , Ajmore-Marsan P , Melchinger A E , Messmer M M , Motto M. Genetic diversity of maize inbred lines within and among heterotic groups revealed by RFLPs. Theor Appl Genet , 1992 , 84 :17 - 25. [15 ]   Dubreuil P , Dufour P , Krejci E , Causse M , de Vienne D , Gallais A , Charcosset A. Organization of RFLP diversity among inbred lines of maize representing the most significant heterotic groups. Crop Sci , 1996 , 36 :790 - 799. [16 ]  Cardy B J , Kannenberg L W. Allozyme variability among maize inbreds lines and hybrids : applications for cultivator identification. Crop Sci , 1982 , 22 :1016 - 1020. [ 17 ]   Pogson G H , Mesa K A , Boutilier R G. Genetic population structure and gene flow in the Atlantic cod Gadus morhua : A comparison of allozyme and nuclear RFLP loci. Genetics , 1995 , 139 :375 - 385. [18 ]  Mumm R H , Dudely J W. A classification of 148 U. S. maize inbreds : I. Cluster analysis based on RFLPs. Crop Sci , 1994 , 34 :842 - 851.

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