Genome mapping in plants

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Andrew H. Paterson and Rod A. Wing

Texas A & M University, College Station, USA

Genome mapping permits the study of morphological, physiological, and developmental processes in which genetic variants exist, and requires minimal a priori information. Further exploitation of the polymerase chain reaction, yeast artificial chromosomes, and comparative analysis of distantly related taxa, will contribute greatly to the fundamental understanding of plant biology

and crop production.

Current Opinion in Biotechnology 1993, 4:142-147

Introduction Genetic mapping

G e n o m e mapping, a synthesis of concepts from classical genetics using tools from molecular biology and methods from biometry, is a powerful approach for the study of plant biology. Genome mapping is rooted in classical genetic linkage analysis, but recent technological advances facilitate the mapping of genes responsible for either simple or complex phenotypes.

Plants are well suited to genetic mapping because of their short generation times, the ease with which large populations can be grown, and their amenabil- ity to artificial crosses. Extensive collections of variants in plant morphology, physiology, and development are available that provide fertile sources of genes for study.

Map-based cloning (that is, the cloning of genes un- derlying discernible p h e n o t y p e s based upon map position) facilitates the isolation of genes affecting processes o f developmental a n d / o r economic importance, with minimal a priori information. Map-based cloning in higher plants is complicated by physically large genomes, prominent repetitive DNA fractions, and polyploidy. Consequently, many developmentally im- portant genes are b e i n g cloned in plants such as Ara- bidopsis, by insertional mutagenesis [1] or subtractive hybridization [2]. Crop plants, however, are cultivated for attributes that are n o t f o u n d in model systems, such as the cotton fiber, maize 'ear', or tomato 'fruit' (berry).

The cloning of g e n e s associated with such attributes, which are the basis o f agricultural productivity, will re- quire the d e v e l o p m e n t o f high-density restriction fragment length p o l y m o r p h i s m (RFLP) maps and yeast arti- tic.iN c h r o m o s o m e (YAC) libraries for major crops and their close relatives.

Plant genetic maps

Detailed genetic maps, based largely u p o n RFLPs, have b e e n constructed for many plants [3]. The most outstanding among these are the maps of tomato (1400 markers distributed over 12 chromosomes) [4"o], and Arabidopsis (500 markers distributed over five chro- mosomes) [5-7]. Recent additions to the growing list of plant genetic maps include conifer [8], loblolly pine [9], barley [10], peanut [11], Brassica rapa [12], rye [13], wheat [14], Cuphea [15], sugarcane (B Sobral, personal communication) and cotton (AH Paterson, unpublished data).

The integrity of a genetic map can b e assessed sta- tistically [16], but biological tests have b e e n reported recently. Mapping of length polymorphisms in sub- telomeric tandem arrays of a 162 base pair element s h o w e d that the genetic maps of four tomato chromosomes are within 5-10 cM of the physical c h r o m o s o m e ends [17]. This is in contrast to recent results from in situ hybridization of m a p p e d low c o p y n u m b e r clones to rice chromosomes, suggesting that the genetic map falls short of the physical c h r o m o s o m e ends [18]. This conflict has yet to be clearly resolved.

Most primary genetic maps of plants have b e e n made in pedigrees chosen for their high DNA marker allele diversity. While m a n y of these crosses harbor agri- culturally useful genes, they are unlikely to p r o d u c e genotypes suited to the needs of the producer, or to the tastes of the consumer. The advantage of using wide crosses for genetic mapping is a consequence of the fact that the elite gene pools of many impor- tam crops are genetically narrow [19]. This indicates that there is an immediate, practical n e e d for DNA

Abbreviations

PCR--polymerase chain reaction; QTL--quantitative trait locus; RAPD--randomly amplified polymorphic DNA;

RFLP~restriction fragment length polymorphism; STM--sequence-tagged microsatellite; YAC--yeast artificial chromosome.

142 © Current Biology Ltd ISSN 0958-1669

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markers that facilitate the genetic analysis of closely related individuals. Solutions to the problem of minimal genetic variation are available, using hypervariable DNA markers associated with arrays of short tandemly repeated sequences [20]. Recent developments have streamlined identification of such markers, and maps of the h u m a n [21"], mouse [22"], and rat [23] g e n o m e s n o w include polymerase chain reaction (PCR) based sequence-tagged microsatellites (STMs). The construction of genomic DNA libraries enriched for STMs was described recently [24]. These allele-rich markers serve the needs of both genetic and physical mapping, and are present in many plants [25].

PCR-based genotyping promises to streamline genetic mapping [26]. A limitation of PCR-based genotyping is that the d e v e l o p m e n t of STMs requires a large invest- ment in sequencing. Randomly amplified polymorphic DNA (RAPD) PCR [27] and arbitrary primer PCR [28]

minimize this cost b y using primers of quasi-arbitrary s e q u e n c e for DNA amplification. One genetic linkage map based largely on RAPDs has b e e n published [7], and another based u p o n arbitrary primer PCR is under- way (B Sobral, personal communication). Dominant inheritance of most RAPD markers sacrifices much information in F2 populations [29]. Further, the reliability of many RAPD markers may not be sufficient for the stringent requirements of linkage mapping, although arbitrary primer PCR markers appear to be more reliable. While the limitations of RAPDs are partially alleviated in homozygous [7] or hemizygous [30] populations, we believe that RAPDs will only find limited use in the construction of primary genetic maps. How- ever, w e emphasize that PCR using arbitrary primers is valuable for enriching predefined genomic regions for DNA markers.

Comparative mapping of plants

Many DNA sequences that e n c o d e proteins are conserved across a wide range of organisms, while non- coding sequences are more freely divergent. Ge- netic mapping of conserved DNA sequences (such as cDNAs) permits the investigation of the order of genes along chromosomes in distantly related taxa. Through comparative mapping, parallelism in gene order (syn- teny) along the chromosomes, as well as breakpoints responsible for differences in gene order, have b e e n demonstrated for tomato and potato [4"',31,32], and sorghum and maize [33]. Comparative mapping sug- gests that remarkably few macroevolutionary events may distinguish plant species. Comparative maps have practical applications too: b y extrapolating map information from one taxon to another, efficient high-density mapping of related taxa can be done simultaneo- usly [3,31,32].

Like cDNAs, some sequence tagged sites are conserved across taxa, permitting PCR to contribute to comparative mapping [34"q. Successful PCR amplification of 30 million year old specimens [35"q adds another di- mension to comparative mapping - a vertical picture through time, as well as a horizontal picture across ex-

Genome mapping in plants Paterson and Wing 143

tant taxa. Comparative mapping may help to unravel the genetic complexities o f polyploids. Wheat, soy- bean, cotton, and other important crops are polyploid, harboring two or more genomes that are distantly related but do not normally pair during meiosis. In the cotton RFLP map (AH Paterson, unpublished data), about 10% of RFLP markers reveal polymorphism at corresponding loci o n each of the two genomes. These markers provide a framework for establishing relation- ships b e t w e e n the two genomes. As these relation- ships b e c o m e clear, each DNA p r o b e m a p p e d to one g e n o m e will also, in effect, be m a p p e d to the other.

The d e v e l o p m e n t of high-density maps for cotton and other polyploids will b e accelerated b y delineating re- lationships b e t w e e n h o m e o l o g o u s chromosomes.

Phenotype mapping and gene tagging

Phenotype mapping is the primary justification for con- structing genetic maps in plants. Closely linked DNA markers facilitate the indirect selection of traits that are difficult to measure, and provide a starting point for map-based cloning of genes of developmental a n d / o r economic importance. DNA markers linked closely to simply inherited traits can b e isolated efficiently using RAPD PCR on near-isogenic lines [36-]. Recently, this powerful technique has b e e n extended to the enrich- ment of any genomic region for DNA markers, using synthetic DNA pools [37",38"]. New markers have b e e n isolated that are linked to the tomato developmental mutations jointless and never-ripe [38.], and lettuce d o w n y mildew resistance loci [37"].

The DNA pooling approach raises the possibility of isolating markers for quantitative trait loci (QTLs) [37°].

This is especially appealing, as QTL mapping requires large populations to discern small phenotypic effects of numerous unlinked loci. Both theoretical expecta- tions and post hoc analysis of previous QTL mapping results, suggest that only QTLs with unusually large effects can be detected using DNA pools (G Wang and AH Paterson, unpublished data). However, once QTLs have b e e n m a p p e d b y current methods [39,40",41], synthetic DNA pools are an excellent means of enriching the genomic region of a QTL for DNA markers. Such markers might be valuable for high-resolution mapping of the QTL [42] or introgression of the QTL into different genotypes.

Physical mapping and map-based cloning

Pulsed-field electrophoresis [43] and YAC DNA vectors [44] permit large regions of plant genomes to be dissected and cloned. These tools allow genes to be isolated based solely o n their genetic map position.

Megabase DNA preparation

A reliable m e t h o d for the isolation of relatively intact, unsheared plant DNA is a prerequisite for pulsed-field

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electrophoresis a n d YAC cloning. Megabase DNA isolation procedures are available for m a n y plants, the most recent additions being s o y b e a n [45], rice [46], wheat, barley and rye [47]. The recurring method is to e m b e d plant protoplasts in agarose plugs, followed b y lysis, proteinase digestion, and washing. Recently, We devel- o p e d a procedure, a d a p t e d from [48], for e m b e d d i n g plant protoplasts in agarose microbeads, which offers significant advantages over plugs (RA Wing, S-S Woo, VK Rastogi, H-B Zhang, AH Paterson, SD Tanksley, unpublished data).

RFLP maps, cosmids and YACs, provide a 'local' v i e w o f the g e n o m e . An overlapping cosmid m a p comprising 90-95% of the Arabidopsis g e n o m e has b e e n con- structed [57]. Recently H w a n g et al. [58] described pre- liminary data to assemble a set of overlapping YACs for the entire Arabidopsis genome. The authors iso- lated 125 YACs using RFLPs across the five linkage groups. These YACs represent 30% of the Arabidop- sis genome. Ultimately, the authors plan to assemble a blot comprising the m i n i m u m n u m b e r of YACs to over- lap the entire g e n o m e , to aid in genetic m a p p i n g and c h r o m o s o m e walking.

Genetic versus physical distance

Once molecular markers have b e e n s h o w n to be genetically linked to a target gene, it is p r u d e n t to es- tablish the relationship b e t w e e n genetic and physical distance in the region surrounding the gene. This information will h e l p to determine a c h r o m o s o m e walk or jump. The average relationship b e t w e e n the genetic and physical distance of a g e n o m e is readily calculated from the g e n o m e size and length of the genetic map.

However, actual values for any specific location vary widely from the average. In the tomato, i cM aver- ages 900 kb, b u t in the Tm2a region of c h r o m o s o m e 9, I cM is 4 - 1 6 M b [49]. This physical distance is currently well b e y o n d the capabilities of m a p - b a s e d cloning. In wheat, w h e r e the k b : c M ratio is m u c h larger than in tomato, I cM is approximately equal to 1 Mb in the region of the 0c-amylase gene o n c h r o m o s o m e 6 [47].

Yeast artificial chromosome libraries

Since the demonstration that large human DNA fragments can b e maintained in YACs [44] m a n y groups have set out to m a k e plant YAC libraries. YAC libraries have b e e n constructed for Arabidopsis [50,51], tomato [52], maize [53] a n d rice (Y U m e h a r a et al. Abstract

#141, Plant G e n o m e I, San Diego, N o v e m b e r 9-11, 1992). In tomato, Martin et al. [52] obtained 22000 clones and s c r e e n e d half of the library with RFLP markers tightly linked to two disease resistance loci, Tm2a and/:'to. Five YACs w e r e isolated in this screen, which mark starting points for c h r o m o s o m e walks to these genes. Recently, a maize YAC library with three haploid g e n o m e equivalents w a s constructed [53]. The library w a s assembled in such a w a y that it can be rapidly screened b y PCR [54]. Richards et al. [551 re- cently constructed a half-YAC library and isolated two biologically functional Arabidopsis thaliana telomeres in yeast.

Complete physical maps

Physical m a p s are valuable in studying the organization a n d evolution of plant c h r o m o s o m e s . In situ hy- bridization provides a 'global' v i e w of g e n o m e organization [56]. Contig maps, a s s e m b l e d using high-density

Gene identification

The most direct a p p r o a c h to g e n e identification from a candidate YAC or cosmid is to c o m p l e m e n t a mutant b y transformation. Giraudat et al. [59] recently d e m o n - strated mutant c o m p l e m e n t a t i o n of the abi3 g e n e using a subclone from o n e of three overlapping cosmids isolated using a linked RFLP. A YAC or a cosmid can b e u s e d as a p r o b e to identify cDNAs specific to the candidate region. Mutant and normal cDNAs can then b e s e q u e n c e d to look for potential mutations. The best candidate cDNA can then b e u s e d for mutant com- plementation, or to create a mutation using antisense technology. Arondel et al. [60"] recently isolated a set o f overlapping YACs which c o v e r e d the fad3 locus of Arabidopsis. One YAC was used to screen a cDNA li- brary m a d e from developing seeds from a closely related species (Brassica napus). A heterologous cDNA w a s isolated and s h o w n to c o m p l e m e n t the fad3 allele.

W h e n no cDNA can be found, the YAC insert must b e subcloned into overlapping fragments, and com- plementation attempted with each subclone indepen- dently. This is time-consuming and labor-intensive.

Several groups h a v e demonstrated stable integration [61-63] or c o m p l e m e n t a t i o n [64] of m a m m a l i a n mutations with entire YAGs. Transfer of w h o l e YACs into plants will streamline g e n e identification.

Conclusion

For m u c h of the 20th century, biologists h a v e b e e n aware of the potential that genetic markers hold for the investigation of c o m p l e x questions in biology. The novel field of g e n o m e m a p p i n g n o w has a sufficient basis of technology and information to realize this potential in a few well-studied plants. Exploitation of comparative m a p information will p r o m o t e continued technological improvement, and facilitate extension of g e n o m e m a p p i n g to tess facile species. We believe that the next f e w years will provide tangible results of g e n o m e m a p p i n g progress in the f o r m of cloned genes, i m p r o v e d cultivars, and a better understanding of plant biology.

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Genome mapping in plants Paterson and Wing 145

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By making two synthetic DNA pools from a segregating population, one pool defining one genotype (e.g. disease resistance or an interval defined by two RFLPs containing DNA from one parent) and a second pool defining the other genotype (e.g disease susceptibility or a interval defined by two RFLPs containing DNA from the other parent) the DNA equivalent of a pair of near isogenic lines can be assembled in a test tube. The pools can then be screened for DNA polymorphisms as can near-isogenic lines.

39. PATERSON AH, LANDER ES, HEWITF JD, PETERSON S, LINCOLN SE, TANKSLEY SD: R e s o l u t i o n o f Q u a n t i t a t i v e Traits i n t o M e n d e l i a n Factors b y U s i n g a C o m p l e t e Linkage Map o f R e s t r i c t i o n F r a g m e n t L e n g t h P o l y m o r p h i s m s . Na-

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40. PATERSON AH, DAMON S, HEWIT3 ~ JD, ZAMm D, LINCOLN SE, LANDER ES, TANKSLEY SD: M e n d e l i a n F a c t o r s Underly- i n g Q u a n t i t a t i v e Traits i n Tomato: C o m p a r i s o n Over Species, G e n e r a t i o n s , a n d E n v i r o n m e n t s . Genetics 1991, 127:181-197.

Extends previous QTL mapping results to analysis of gene action, and gives tentative indications of common QTLs accounting for phenotypic variation in diverse pedigrees.

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42. PATERSON AH, DEVEIINA JW, LANINI B, TANKSLEY SD: Fine Mapping o f Quantitative Trait Loci U s i n g Selected O v e r l a p p i n g R e c o m b i n a n t C h r o m o s o m e s , i n a n Inter- s p e c i e s C r o s s o f Tomato. Genetics 1990, 124:735-742.

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44. BURKE DT, CARLE GF, OLSON MV: C l o n i n g o f Large Seg- m e n t s o f E x o g e n o u s DNA i n t o Yeast b y M e a n s o f Ar- tificial C h r o m o s o m e Vectors. Science 1987, 236:806-811.

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46. SOBRAL BWS, HONEYCLrlT RJ, ATHERLY AG, MCCLELLAND M: A n a l y s i s o f Rice ( O r y z a s a t i v a L.) G e n o m e Us- i n g Pulsed-Field E l e c t r o p h o r e s i s a n d R a r e Cutting R e s t r i c t i o n E n d o n u d e a s e s . Plant Mol Biol Reports 1990, 8:253-275.

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49. GANAL MW, YOUNG ND, TANKSLEY SD: P u l s e d Field Gel E l e c t r o p h o r e s i s a n d P h y s i c a l M a p p i n g o f Large DNA F r a g m e n t s i n t h e Tin-2a R e g i o n o f C h r o m o s o m e 9 i n Tomato. Mol Gen Genet 1989, 215:395-400.

50. WARD ER, JEN GC: I s o l a t i o n o f Single-Copy-Sequence C l o n e s f r o m a Yeast Artificial C h r o m o s o m e Library o f R a n d o m l y - S h e a r e d Arabidopsis thaltana DNA. Plant Mol Biol 1990, 14:561-568.

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52. MARTIN GB, GANAL MW, TANKSLEY SD: C o n s t r u c t i o n o f a Yeast Artificial C h r o m o s o m e Library o f T o m a t o and I d e n t i f i c a t i o n o f C l o n e d S e g m e n t s L i n k e d to Two Dis- e a s e R e s i s t a n c e Loci. Mol Gen Genet 1992, 223:25-32.

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AH Paterson a n d RA Wing, Texas A&M University, Department o f Soil a n d Crop Sciences, College o f Agriculture a n d Life Sciences, College Station, Texas 77843-2474, USA.