Conversion of a rice CMS maintainer into a photo- or thermo-sensitive genetic male sterile line

A maintainer line of 3-line hybrid rice commonly presents a certain genetic distance to a 2-line restorer line, but in many cases, 2-line restorer lines present defects upon recovery of the object cytoplasmic male sterile (CMS) line of the maintainer line, which impedes the utilization of their heterosis. Here, we report a strategy and an example of converting a maintainer into a photoperiod/temperature-sensitive genic male sterile (P/TGMS) line with an almost identical genetic background, thus maximizing the heterosis. Firstly, through treatment of maintainer line T98B with ⁶⁰C_O-γ irradiation, we identified the TGMS line T98S, which is sterile at higher temperatures and fertile at lower temperatures. Secondly, the T98S line was proven to be identical to T98B with regard to genetic background via an examination of 48 parental polymorphous SSR markers and exhibited excellent blossom traits similar to those of T98B, with an extensive forenoon flowering rate of 75.92% and a high exertion rate of 64.59%. Thirdly, in a combination test, three out of six hybrids from T98S crossed with 2-line restorer lines showed a yield increase of 6.70–15.69% for 2 consecutive years. These results demonstrated that the strategy can generate a new P/TGMS line with strong general combining ability (converted from a maintainer line), thus helping to increase the genetic diversity of male sterile heterotic groups.     

Grouping of tropical mid-altitude maize inbred lines on the basis of yield data and molecular markers

The classification of maize inbred lines into heterotic groups is an important undertaking in hybrid breeding. The objectives of our research were to: (1) separate selected tropical mid-altitude maize inbred lines into heterotic groups based on grain yield data; (2) assess the genetic relationships among these inbred lines using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers; (3) examine the consistency between yield-based and marker-based groupings of the inbred lines. Thirty-eight tropical mid-altitude maize inbred lines were crossed to two inbred line testers representing the flint and dent heterotic pattern, respectively. The resulting testcrosses were evaluated in a trial at three locations for 2 years. Significant general combining ability (GCA) and specific combining ability (SCA) effects for grain yield were detected among the inbred lines. The tester inbred lines classified 23 of the 38 tested inbred lines into two heterotic groups based on SCA effects and testcross mean grain yields. This grouping was not related to endosperm type of the inbred lines. The outstanding performance of testcrosses of the remaining 15 inbred lines indicates the presence of significant genetic diversity that may allow the assignment of the lines into more than two heterotic groups. Diversity analysis of the 40 maize inbred lines using AFLP and SSR markers found high levels of genetic diversity among these lines and subdivided them into two main groups with subdivision into sub-groups consistent with breeding history, origin and parentage of the lines. However, heterotic groups formed using yield-based combining ability were different from the groups established on the basis of molecular markers. Considering the diversity of the genetic backgrounds of the mid-altitude inbred lines, the marker-based grouping may serve as the basis to design and carry out combining ability studies in the field to establish clearly defined heterotic groups with a greater genetic similarity within groups.Communicated by H.H. Geiger     

Evaluating genetic relationships between tropical maize inbred lines by means of AFLP profiling

Diversity among tropical maize inbred lines that compose breeding programs, is not well known. The lack of this information has made the arrangement of heterotic groups to be used for breeding purposes difficult. Methods of molecular analysis have been used as efficient alternatives for evaluating genetic diversity, aiming at heterotic group arrangement and acquisition of new hybrids. In this study, AFLP (amplified fragment length polymorphism) was used to investigate the genetic relationships among 96 tropical maize inbred lines from two different origins. The polymorphism level among the genotypes and the possibility of their allocation in heterotic groups were evaluated. Besides, correlations among genetic diversity and flowering time were analyzed. Nine primer combinations were used to obtain AFLP markers, producing 638 bands, 569 of which were polymorphic. Genetic similarities (GS), determined by Jaccard's similarity coefficient, varied from 0.345 to 0.891, with an average of 0.543. The dendrogram based on the GS and on the UPGMA cluster method did not separate the inbred lines in well-defined groups. Aiming at separating the lines into more accurate groups, Tocher's optimization procedure was carried out, 17 groups being identified. Association between flowering time and germplasm pools was detected. AFLP showed itself to be a robust assay, revealing a great power of detection of genetic variability in the tropical germplasm, and also demonstrated to be very useful for guiding breeding programs.     

Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: genetic diversity among oilseed inbred lines

 Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints. The AFLP diversity of sunflower has not been described, and much of the public germ plasm of sunflower has not yet been fingerprinted. Our objectives were to: (1) estimate genetic similarities, polymorphism rates, and polymorphic information contents (PICs) for AFLP markers among elite public oilseed inbred lines, and (2) assess the genetic diversity of inbred lines using genetic similarities estimated from AFLP fingerprints. We produced fingerprints for 24 public inbred lines of sunflower (Helianthus annuus L.) using six AFLP primer combinations. These primers produced a total of 359 AFLP markers or about 60 markers per primer combination. Genetic similarities ranged from 0.70 to 0.91, polymorphism rates ranged from 7 to 24%, and PICs ranged from 0.0 to 0.5. Genetic similarities were lower overall for maintainer (B)×restorer (R) crosses than for B×B or R×R crosses. Principal-coordinate and cluster analyses separated lines into two groups, one for B-lines and another for R-lines. These groupings illustrate the breeding history and basic heterotic pattern (B×R) of sunflower and the widespread practice of using B×B and R×R crosses to develop new lines. There were, nevertheless, distinct subgroups within these groups. These subgroups may represent unique heterotic groups and create a basis for formally describing heterotic patterns in sunflower. Received: 10 June 1996 / Accepted: 4 April 1997     

红莲型杂交稻(红莲2号)及其骨干亲本的RAPD分析与鉴定

利用RAPD技术,从248个随机寡核苷酸引物（10－mer）中筛出18个引物对红莲型杂交稻组合红莲2号及其亲本（T－07A、T－07B、YD6－05）,另6个红莲型胞质不育系的骨干恢复和汕优63及其亲本共14份水稻材料进行分析。共检测到173个多态性标记。聚类分析结果表明：不育系与保持系间因核背景相似,遗传差异很小;杂种（F1）的基因型更倾向于恢复系;恢复系与保持系间遗传距离的相对较大,但各恢复系之间的遗传距离较小。利用这些标记能有效地地区交组合中不育系,保持系、恢复系和杂种（F1）。     

Determination of heterotic groups for tropical Indica hybrid rice germplasm

Key message

Two heterotic groups and four heterotic patterns were identified for IRRI hybrid rice germplasm to develop hybrid rice in the tropics based on SSR molecular data and field trials.

Abstract

Information on heterotic groups and patterns is a fundamental prerequisite for hybrid crop breeding; however, no such clear information is available for tropical hybrid rice breeding after more than 30 years of hybrid rice commercialization. Based on a study of genetic diversity using molecular markers, 18 parents representing hybrid rice populations historically developed at the International Rice Research Institute (IRRI) were selected to form diallel crosses of hybrids and were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. Results revealed that inter-group hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IRRI B- and R-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IRRI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IRRI hybrid rice parents.     

Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

A set of morphological traits and SSR markers were used to determine the genetic relationship among 12 elite thermosensitive genic male sterile (TGMS) lines developed at three different research institutions of India. Agro-morphological data recorded on 20 morphological traits revealed a wide base of genetic variation and a set of four morphological traits could distinguish most of the TGMS lines. Analysis with 30 SSR markers (20 EST-SSRs and 10 genomic SSRs) revealed 27 markers to be polymorphic, amplifying a total of 83 alleles. Each SSR marker amplified 2-6 alleles with an average of 2.76 alleles per marker and a PIC value varying from 0.54 to 0.96. Cluster analysis based on SSR and morphological data clearly differentiated the lines according to their source of origin. Correlation analysis between morphological and molecular data revealed a very poor association (r = 0.06), which could be attributed to selection pressure, genetic drift, sampling error and unknown relationship among related lines. The SSR markers discriminated the genotypes distinctly and quantified the genetic diversity precisely among the TGMS lines. Data on the yield per plant indicated that the genotypes grouping under a similar cluster showed same heterotic behaviour as compared to the genotypes from different clusters when crossed to similar pollinators.     

红麻UG93细胞质雄性不育系、保持系及恢复系间的遗传多样性分析

利用8条核基因组ISSR引物和7对叶绿体基因组SSR引物(cpSSR),对9对红麻UG93细胞质雄性不育系/保持系及5个恢复系的细胞核、细胞质遗传多样性进行分析.结果表明:各材料的核基因组遗传相似系数在0.333～1.000之间,其中保持系间、保持系和恢复系间、恢复系间的平均相似系数分别为0.583、0.689和0.8...     

Application of SSR markers for molecular characterization of hybrid parents and purity assessment of ICPH 2438 hybrid of pigeonpea [<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millspaugh]

With an objective of achieving a breakthrough in the productivity of pigeonpea, a hybrid breeding technology based on elements of the cytoplasmic-nuclear male-sterility (CMS) system and partial natural out-crossing has recently been developed. However, there is no molecular diversity information available on parental lines of hybrids being generated at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). This study deals with the use of 148 simple sequence repeat (SSR) markers, including 32 novel markers reported here for the first time, on 159 A (cytoplasmic male sterile), B (maintainer) and R (fertility restorer) lines. In total, 41 (27.7%) markers showed polymorphism with 2 to 6 (average 2.6) alleles and 0.01 to 0.81 (average 0.34) polymorphism information content (PIC) value. Of these polymorphic markers, 22 SSR markers showed polymorphism between A (ICPA 2039) and R (ICPR 2438) lines of the commercial hybrid (ICPH 2438); however, only 21 of these SSR markers showed the same profile between A (ICPA 2039) and B (ICPB 2039) lines. Finally, two SSR markers, CCB4 and CCttc006, were found most suitable for purity assessment of hybrid seeds of the ICPH 2438 hybrid. The utility of these two diagnostic SSR markers has been demonstrated by using seed lots of this hybrid from two sources, ICRISAT and Mahabeej. It is anticipated that molecular diversity information generated on parental lines of hybrids under development, and identification of the two most suitable markers for testing the purity of hybrid seeds of ICPH 2438, will facilitate the pigeonpea hybrid breeding programme.     

Genetic diversity and its relationship to hybrid performance in maize as revealed by RFLP and AFLP markers

 The challenge to maize breeders is to identify inbred lines that produce highly heterotic hybrids. In the present study we surveyed genetic divergence among 13 inbred lines of maize using DNA markers and assessed the relationship between genetic distance and hybrid performance in a diallel set of crosses between them. The parental lines were assayed for DNA polymorphism using 135 restriction fragment length polymorphisms (RFLPs) and 209 amplified-fragment polymorphisms (AFLPs). Considerable variation among inbreds was detected with RFLP and AFLP markers. Moreover AFLPs detect polymorphisms more efficiently in comparison to RFLPs, due to the larger number of loci assayed in a single PCR reaction. Genetic distances (GDs), calculated from RFLP and AFLP data, were greater among lines belonging to different heterotic groups compared to those calculated from lines of the same heterotic group. Cluster analysis based on GDs revealed associations among lines which agree with expectations based on pedigree information. The GD values of the 78 F₁ crosses were partioned into general (GGD) and specific (SGD) components. Correlations of GD with F₁ performance for grain yield were positive but too small to be of predictive value. The correlations of SGDs, particularly those based on AFLP data, with specific combining-ability effects for yield may have a practical utility in predicting hybrid performance. Received: 15 August 1997 / Accepted: 19 September 1997     

Genetic diversity analysis of maintainer and restorer accessions in upland cotton (Gossypium hirsutum L.)

Genetic diversity amongst 91 upland cotton accessions (50 maintainer, ‘B’ and 41 restorer ‘R’ lines) and three wild species viz., G. aridum, G. thurberi and G. anomalum was analyzed using SSR and RAPD markers. A total of 53 primers (30 SSR and 23 RAPD) were sampled for screening 94 accessions, of which 26 SSR and 17 RAPD primers were polymorphic. Average polymorphism detected by SSR, RAPD and SSR + RAPD markers was 72.5, 62 and 66.66 per cent, respectively. A unique marker CIR-200₂₆₀ that distinguishes G. thurberi from all upland accessions has been identified. Similarity coefficient values within and between B and R lines ranged from 0.65–0.95, 0.61–0.98 and 0.53–0.93 for SSR and 0.72–0.98, 0.73–0.97 and 0.69–0.98 for RAPD markers. UPGMA cluster analysis was consistent with the pedigree and genotypic background of the accessions. RAPD and SSR matrices showed significant positive product moment correlation (r?=?0.93 and 0.92) with the RAPD + SSR combined data matrix, respectively. The result indicates a moderate level of genetic diversity in B and R accessions of upland cotton. Genetically diverse combinations were identified to further evaluate heterotic performance. The maintainer, AKH-108, AKH-118 and AKH-2173; and restorer AKH-31 and AKH 4943 accession were identified as most distinct and divergent, could be used as candidate parental genotypes in hybrid and varietal development programme and also development of mapping population for trait mapping in cotton.     

Prediction of hybrid grain yield performances in Indica Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) with effect-increasing loci

One hundred and fifty-one rice hybrids produced in two sets of half-dialell crosses and their parents (13 cytoplasmic male sterile lines and 19 restorers) were used to predict the F₁ performances of seven yield traits through the parental genetic distances (GD) based on SSR markers. The positive loci (PL) and effect-increasing loci (IL), which were screened from SSR polymorphic loci by the F₁ traits of 32 parents, together with total loci (TL), were utilized to estimate parental GD and the models were found to predict the traits of hybrids derived from different parents, fixed parents, and different environments, respectively. The results were as follows: (1) 550 polymorphic loci were detected from 174 SSR markers: a dendrogram based on these loci could separate all the sterile and restorer lines used in the present study, which indicated that parental genetic diversity of F₁ was large; (2) the correlations between F₁ traits and parental GDs based on IL ranged from 0.61 to 0.87 with a mean of 0.76, and they were higher than those on TL or on PL; (3) predictions based on IL for F₁ traits (except grain weight per plant) derived from different environments were ideal, but worse for F₁ traits derived from different parents; and (4) IL was more effective than TL and PL in predicting traits of F₁ with fixed parents, and predictions for fixed restorer combinations were more effective than those for fixed sterile line combinations. These results should facilitate molecular prediction for hybrid yield and other traits by means of both elite sterile and restorer lines.     

DNA divergence as a criterion of a sweet pepper (Capsicum annuum L.) selection for heterosis

The identification of perspective parental lines for the creation of high-yield hybrids is the most labor-consuming stage of selection, because it needs extensive trials of combining ability. Based on evaluation of the genetic divergence of the parental lines, the prediction accuracy of F₁ hybrids performance was investigated. The value of the divergence was calculated using biometric and molecular methods, such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD). Based on estimates of divergence, 10 lines were chosen for cyclic cross (scheme I) and testcross (scheme II). In most crosses, the F₁ hybrids were significantly superior to the parents in the main economically valuable traits. The level of heterosis was higher among hybrids of scheme I. Analysis of the relationship between parental divergence and F₁ performance showed that the hybrid productivity of scheme I was predetermined by ISSR divergence in 86%, and productivity was caused by RAPD divergence in 69%, whereas the F₁ yield of scheme II was not related to the value of genetic distances. Since the values of DNA divergence were closely associated both with midparent level and F₁ performance, we assumed that part of the polymorphic DNA fragments of the parental lines of scheme I is related to heterotic loci (HTL), which may be considered potential key markers for the heterotic selection of the sweet pepper.     

Improving blast resistance of maintainer line DRR 9B by transferring broad spectrum resistance gene Pi2 by marker assisted selection in rice

Hybrid rice technology offers great promise to further enhance rice production and productivity for global food security. Improving hybrid rice parental lines is the first step in developing heterotic rice hybrids. To improve resistance against blast disease, a maintainer line DRR 9B was fortified with a major broad-spectrum blast resistance gene Pi2 through marker-assisted selection. The rice blast caused by Magnaporthe oryzae is a major disease and can cause severe yield losses upto 100%. The NILs of Samba Mahsuri namely BA-23-11-89-12-168 possessing Pi2 was utilized as a donor parent. The PCR-based molecular marker tightly linked to Pi2 gene was used for the foreground selection at BC₁F₁ generation. The molecular marker tightly linked to the major fertility restorer gene Rf4 was used for negative selection (i.e., selection of plants possessing non fertility restoring alleles) at BC₁F₁ generation to identify maintainer lines. The positive plants with Rf4 gene were added to the restorer pool for restorer line development. At each stage, MAS for Pi2 coupled with stringent phenotypic selection for agro-morphological and grain quality traits were exercised. At BC₁F₃ generation, one hundred families were screened against blast disease at uniform blast nursery (UBN) and selected resistant lines were advanced to next generations. In the BC₁F₅ generation plants were subjected to agro-morphological evaluation for yield and yield-contributing traits. The selected plants at BC₁F₅ generation were crossed with DRR 9A to assess the maintainer ability of blast resistance lines and for further CMS line conversion for hybrid rice breeding for developing blast resistance rice hybrids.     

Trends in genetic diversity among European maize cultivars and their parental components during the past 50 years

It has been claimed that the system that delivers the products of plant breeding reduces the diversity of cultivated varieties leading to an increased genetic vulnerability. The main goal of our study was to monitor the temporal trends in genetic diversity over the past five decades among maize cultivars with the largest acreage in Central Europe. Our objectives were to (1) investigate how much of the genetic diversity present in important adapted open-pollinated varieties (OPVs) has been captured in the elite flint germplasm pool, (2) examine changes in the genetic diversity among the most important commercial hybrids as well as in their dent and flint parents, (3) analyze temporal changes in allele frequencies between the dent and flint parental inbreds, and (4) investigate linkage disequilibrium (LD) trends between pairs of loci within the set of parental dent and flint lines. We examined 30 individuals of five prominent OPVs from Central Europe, 85 maize hybrids of economic importance, and their dent and flint parental components with 55 SSRs. LD was significant at probability level P=0.01 for 20.2% of the SSR marker pairs in the 82 dent lines and for 17.2% in the 66 flint lines. The dent and flint heterotic groups were clearly separated already at the beginning of hybrid breeding in Central Europe. Furthermore, the genetic variation within and among varieties decreased significantly during the five decades. The five OPVs contain numerous unique alleles that were absent in the elite flint pool. Consequently, OPVs could present useful sources for broadening the genetic base of elite maize breeding germplasm.     

RFLP studies of genetic relationships among inbred lines of the cultivated sunflower,Helianthus annuus L.: evidence for distinct restorer and maintainer germplasm pools

One-hundred-and-eighty-one nuclear DNA probes were used to examine restriction-fragment length polymorphism in inbred lines of the cultivated sunflower (Helianthus annuus L.). The probes were from six libraries: two genomic libraries — one made with PstI and the other with HindIII, and four cDNA libraries — from etiolated plantlets, green leaves, ovaries, petals and anthers. Total DNA from 17 inbred lines representing an overview of the genetic stocks of sunflower, including restorer and maintainer lines of the classical cytoplasmic male sterility, was digested with four different restriction enzymes and probed in 331 probe-enzyme combinations. Of 181 clones analysed, 73 probes were found to be polymorphic. Genetic distances between inbreds were calculated from the resultant proportion of shared bands and submitted to principal component analysis and the UPGMA tree-making method. The RFLP analysis allowed a clear differentiation between restorer and maintainer lines of the cytoplasmic male sterility, together with a grouping of some of the genotypes from the same origin. The analysis of the accuracy of distance estimation as a function of the number of probe-enzyme combinations used, indicates that 40–50 combinations ensure a confidence level of near 95%. Considering the inbreds as representatives of the range of cultivated inbreds, estimates of gene diversity, as well as estimates of average gene diversity between and within the sets of restorer and maintainer lines, were calculated. Estimation of gene diversity showed that the available genetic variability in cultivated sunflower, based on allelic frequencies, is lower than that of other plants (H=0.20). Moreover, we show that the proportion of genetic variability due to the difference between maintainer and restorer lines (D_m) is about 2%.     

Genetic distances revealed by morphological characters,isozymes, proteins and RAPD markers and their relationships with hybrid performance in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Genetic distances (GDs) based on morphological characters, isozymes and storage proteins, and random amplified polymorphic DNAs (RAPD) were used to predict the performance and heterosis of crosses in oilseed rape (Brassica napus L.). Six male-sterile lines carrying the widely used Shaan2A cytoplasm were crossed with five restorer lines to produce 30 F₁ hybrids. These 30 hybrids and their parents were evaluated for seven agronomically important traits and their mid-parent heterosis (MPH) at Yangling, Shaanxi province in Northwest China for 2 years. Genetic similarity among the parents based on 34 isozyme and seven protein markers was higher than that based on 136 RAPDs and/or 48 morphological markers. No significant correlation was detected among these three sets of data. Associations between the different estimates of GDs and F₁ performance for some agronomic traits were significant, but not for seed yield. In order to enhance the predicting efficiency, we selected 114 significant markers and 43 favoring markers following statistical comparison of the mean values of the yield components between the heterozygous group (where the marker is present only in one parent of each hybrid) and the homozygous group (where the marker is either present or absent in both parents of each hybrid) of the 30 hybrids. Parental GD based on total polymorphic markers (GD_total, indicating general heterozygosity), significant markers (GD_sign, indicating specific heterozygosity) and favoring markers (GD_favor, indicating favoring-marker heterozygosity) were calculated. The correlation between GD_favor or GD_sign and hybrid performance was higher than the correlation between GD_total and hybrid performance. GD_sign and GD_favor significantly correlated with plant height, seeds per silique and seed yield, but not with the MPH of the other six agronomic traits with the exception of plant height. The information obtained in this study on the genetic diversity of the parental lines does not appear to be reliable for predicting F₁ yield and heterosis.     

Molecular mapping and inheritance of restoration of fertility (<Emphasis Type="Italic">Rf</Emphasis>) in A4 hybrid system in pigeonpea (<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millsp.)

Key message

We report molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea. We have also developed PCR-based markers amenable to low-cost genotyping to identify fertility restorer lines.

Abstract

Commercial hybrids in pigeonpea are based on A4 cytoplasmic male sterility (CMS) system, and their fertility restoration is one of the key prerequisites for breeding. In this context, an effort has been made to understand the genetics and identify quantitative trait loci (QTL) associated with restoration of fertility (Rf). One F₂ population was developed by crossing CMS line (ICPA 2039) with fertility restorer line (ICPL 87119). Genetic analysis has shown involvement of two dominant genes in regulation of restoration of fertility. In parallel, the genotyping-by-sequencing (GBS) approach has generated ~?33 Gb data on the F₂ population. GBS data have provided 2457 single nucleotide polymorphism (SNPs) segregating across the mapping population. Based on these genotyping data, a genetic map has been developed with 306 SNPs covering a total length 981.9 cM. Further QTL analysis has provided the region flanked by S8_7664779 and S8_6474381 on CcLG08 harboured major QTL explained up to 28.5% phenotypic variation. Subsequently, sequence information within the major QTLs was compared between the maintainer and the restorer lines. From this sequence information, we have developed two PCR-based markers for identification of restorer lines from non-restorer lines and validated them on parental lines of hybrids as well as on another F₂ mapping population. The results obtained in this study are expected to enhance the efficiency of selection for the identification of restorer lines in hybrid breeding and may reduce traditional time-consuming phenotyping activities.

     

Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms

Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.     

Hybrid performance and genetic distance as revealed by the (GATA)4 microsatellite and RAPD markers in pearl millet

 Genetic diversity in five cytoplasmic male-sterile and seven restorer lines of pearl millet was determined by DNA fingerprinting using a (GATA)₄ microsatellite and randomly amplified polymorphic DNAs (RAPDs). A total of 160 polymorphic loci were generated and, based on the polymorphism data, similarity index values ranged from 0.81 to 0.50. Cluster analysis was performed and relationships among these lines revealed that they were not in agreement with the available pedigree data. The per se performance of parents and hybrids was analyzed for days-to-50% flowering, plant height, productive tillers, ear length, ear width, 1000-grain weight and grain yield per plot. Path co-efficient analysis revealed that productive tillers, ear width and days-to-50% flowering had a relatively large positive effect. The correlation values were mostly not significant with respect to genetic distance, except for days-to-50% flowering, ear length and ear width. Our results have indicated that genetic-distance measures based on the (GATA)₄ microsatellite and RAPDs may be useful for the grouping of parents, but not for predicting heterotic combinations, in pearl millet. Received: 3 January 1998 / Accepted: 25 February 1998