Significant genomic introgression from grey junglefowl(Gallus sonneratii)to domestic chickens(Gallus gallus domesticus)

Background Chicken is one of the most numerous and widely distributed species around the world,and many studies support the multiple ancestral origins of domestic chickens.The research regarding the yellow skin phenotype in domestic chickens(regulated by BCO2)likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens.However,beyond the BCO2 gene region,much remains unknown about the introgression from the grey junglefowl into domestic chickens.Therefore,in this study,based on wholegenome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds,we explored the introgression events from the grey junglefowl to domestic chickens.Results We successfully detected introgression regions besides BCO2,including two associated with growth trait(IGFBP2 and TKT),one associated with angiogenesis(TIMP3)and two members of the heat shock protein family(HSPB2 and CRYAB).Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens.Furthermore,we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds,indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained.Additionally,our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens,possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens.Conclusions In summary,our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens,laying the foundation for a deeper understanding of the genetic composition within domestic chickens,and offering new perspectives on the impact of introgression on domestic chickens.

Utilizing resequencing big data to facilitate Brassica vegetable breeding:tracing introgression pedigree and developing highly specific markers for clubroot resistance

Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable species B.rapa and B.oleracea,several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding.However,the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders'most urgent concerns.The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs.Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data.In B.rapa,a major locus CRzi8 underlying the CR of the commercial CR donor‘DegaoCR117’was identified.CRzi8 was further shown to have been introgressed from turnip(B.rapa ssp.rapifera)and that it carried a potential functional allele of Crr1a.The turnip introgression carried CRb^(c),sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B.oleracea CR cultivars with different morphotypes.Within natural populations,variation analysis of linkage intervals of CRzi8,PbBa8.1,CRb,and CRb^(c)yielded easily resolved InDel markers(>20 bp)for these fundamental CR genes.The specificity of these markers was tested in diverse cultivars panels,and each exhibited high reliability in breeding.Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs.

Origins,timing and introgression of domestic geese revealed by whole genome data

Background Geese are among the most important poultry species in the world.The current generally accepted hypothesis is that the European domestic geese originated from greylag geese(Anser anser),and Chinese domestic geese have two origins,most of which originated from swan geese(Anser cygnoides),and the Yili goose originated from greylag geese.To explain the origin and demographic history of geese,we selected 14 goose breeds from Europe and China and wild populations of swan and greylag geese,and whole genome sequencing data were obtained for 74 samples.Results Population structure analysis and phylogenetic trees showed that the wild ancestor of Chinese domestic geese,except for Yili,is the swan geese,and the wild ancestor of Chinese Yili and European domestic geese is greylag geese.Analysis of the demographic history suggests that the domestication of Chinese geese occurred~3499 years ago and that of the European geese occurred~7552 years ago.Furthermore,gene flow was observed between domestic geese and their wild ancestors.Analysis of introgression showed that Yili geese had been introgressed by Chinese domestic geese,and the body size of Yili geese may be influenced by introgression events of some growthrelated genes,including IGF-1.Conclusions Our study provides evidence for the origin of geese at the genome-wide level and advances the understanding of the history of goose domestication and the traits affected by introgression events.

Genome-wide recombination variation in biparental segregating and reciprocal backcross populations provides information for introgression breeding in Brassica napus

Variation in patterns of recombination in plant genomes provides information about species evolution,genetic diversity and crop improvement. We investigated meiotic crossovers generated in biparental segregating and reciprocal backcross populations of the allopolyploid genome of rapeseed(Brassica napus)(AACC, 2n = 38). A structured set of 1445 intercrossed lines was derived from two homozygous de novo genome-assembled parents that represented the major genetic clusters of semi-winter Chinese and winter European rapeseeds, and was used to increase QTL resolution and achieve genomic reciprocal introgression. A high-density genetic map constructed with 6161 genetic bins and anchored centromere regions was used to establish the pattern of recombination variation in each chromosome. Around 93%of the genome contained crossovers at a mean rate of 3.8 c M Mb^(-1), with the remaining 7% attributed to centromeres or low marker density. Recombination hotspots predominated in the A genome, including two-thirds of those associated with breeding introgression from B. rapa. Genetic background might affect recombination variation. Introgression of genetic diversity from European winter to Chinese semi-winter rapeseed showed an increase in crossover rate under the semi-winter environment. Evidence for an elevated recombination rate having historically contributed to selective trait improvement includes accumulation of favorable alleles for seed oil content on hotspots of chromosome A10. Conversely, strong artificial selection may affect recombination rate variation, as appears to be the case with a coldspot resulting from strong selection for glucosinolate alleles on A09. But the cold region would be promptly reactivated by crossing design indicated by the pedigree analysis. Knowledge of recombination hotspots and coldspots associated with QTL for 22 traits can guide selection strategies for introgression breeding between the two gene pools. These results and rich genomic resources broaden our understanding of recombination behavior in allopolyploids and may advance rapeseed genetic improvement.

Production of Partial New-typed Brassica Napus by Introgression of Genomic Components from B. rapa and B. carinata

A breeding strategy for widening the germplasm of Brassica napus was proposed by introgression of the A^r subgenome of B. rapa （A^rA^r） and C^c of B. carinata （B^cB^cC^cC^c） into natural B. napus （AnAncncn）. The progenies with 38 chromosomes that were derived from the self-pollinated seeds of pentaploid hybrids （A^rA^nB^cC^cC^n） were used for further research. Some of the partial new-typed B. napus showed normal meiotic behavior, high portion of germinated pollen and normal embryological development. This indicates that the selected new-typed B. napus had a balanced genetic base. Molecular analysis showed that about 50% of the genome in the new-typed B. napus was replaced by A^r and C^c subgenome from B. rapa and B. carinata. Considering the genetic diversity among different lines of new-typed B. napus, it was deduced that the introgression of the genomic components from B, rapa and B. carinata could widen the genetic diversity of rapeseed.

Breeding by selective introgression: Theory, practices, and lessons learned from rice

Future demands for increased productivity and resilience to abiotic/biotic stresses of major crops require new technologies of breeding by design(BBD)built on massive information from functional and population genomics research.A novel strategy of breeding by selective introgression(BBSI)has been proposed and practiced for simultaneous improvement,genetic dissection and allele mining of complex traits to realize BBD.BBSI has three phases:a)developing large numbers of trait-specific introgression lines(ILs)using backcross breeding in elite genetic backgrounds as the material platform of BBD;b)efficiently identifying genes or quantitative trait loci(QTL)and mining desirable alleles affecting different target traits from diverse donors as the information platform of BBD;and c)developing superior cultivars by BBD using designed QTL pyramiding or marker-assisted recurrent selection.Phase(a)has been implemented massively in rice by many Chinese research institutions and IRRI,resulting in the development of many new green super rice cultivars plus large numbers of ILs in 30+elite genetic backgrounds.Phase(b)has been demonstrated in a series of proof-of-concept studies of high-efficiency genetic dissection of rice yield and tolerance to abiotic stresses using ILs and DNA markers.Phase(c)has also been implemented by designed QTL pyramiding,resulting in a prototype of BBD in several successful cases.The BBSI strategy can be easily extended for simultaneous trait improvement,efficient gene and QTL discovery and allele mining of complex traits using advanced breeding lines from crosses between a common"backbone"parent and a set of elite parents in conventional pedigree breeding programs.BBSI can be relatively easily adopted by breeding programs with small budgets,but the BBSI-based BBD strategy can be fully and more efficiently implemented by large seed companies with sufficient capacity.

Identification for Heat Tolerance in Backcross Recombinant Lines and Screening of Backcross Introgression Lines with Heat Tolerance at Milky Stage in Rice

The present study aimed at breeding new rice germplasms with similar genome but significantly differed in heat tolerance during the grain filling stage.A total of 791 BC1F8 backcross recombinant lines,derived from the cross of Xieqingzao B /N22 //Xieqingzao B,were used as materials.Each rice line was separated evenly into two groups,and the heat tolerance of all rice lines were evaluated at natural high temperature in fields.The rice lines with heat tolerant index higher than 90% or lower than 40% were selected to compare the phenotypic characters and further identify heat tolerance at the early milky stage in a phytotron.Rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were analyzed by 887 simple sequence repeat markers that were evenly distributed on the 12 rice chromosomes.In the result,12(6 pairs) rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were obtained.Molecular marker analysis indicated that the genomic polymorphism between 703T and 704S was the smallest in the 6 pairs of rice lines,with only 16 polymorphic sites,including 22 different alleles.The application of these two backcross introgression rice lines for future study on the mechanisms of heat tolerance in rice at the milky stage will be theoretically beneficial in reducing the interference caused by genetic differences from experimental materials.

Analysis on Genomic Structure Changes and Diversity of Introgression Lines in Dongxiang Wild Rice(Oryza rufipogon Griff.)

[Objective] The aim of the study was to make research on genomic struc- ture variation and variety analysis of Dongxiang wild rice. [Method] Introgression groups of BC1F6 were based on donor of Oryza rufipogon Griff. and receptor of O. sativa sp. indica Kate. Strains of 239 in the group were analyzed on Polymor- phism with the help of 25 couples of SSR primers distributed in 12 pairs of chromo- somes. [Result] Gene fragments of O. rufipogon Griff. were found penetrated in the 25 microsatellite sites and most of the groups kept the parents of Xieqinzao B or DNA sequence of O. rufipogon Griff. The average rate of recurrent homozygous bands was 78.13% in the ILs, but the highest was 94.98% （amplified by primer RM131） and the lowest was 60.25% （RM171）. The average rate of donor homozy- gous bands was 13.37%, but the highest was 32.64% （RM171） and the lowest was 2.93% （RM1095）. There were numerous heterozygous sites in the population and the average heterozygosis rate was 5.62%, while the highest was 10.04%（RM401）. Moreover, we found some parental fragments were lost and some novel fragments were not detected in either parent in BC1F6 population. The average rate of lost bands was 2.88%, while the highest was 13.39% （RM311） and the lowest was 0 （RM401）. The average rate of new bands was 1%. The average of Nei＇s gene di- versity （He） and Shannon＇s Information index （I） were 0.276 and 0.457 respectively in high generation of introgression lines. [Conclusion] The study demonstrated that distant hybridization led to extensive genetic and epigenetic variations in high gener- ation of introgression lines, which expanded the base of genetic variation and laid an important foundation for rice improvement and germplasm innovation.

Development and Identification of Introgression Lines from Cross of Oryza sativa and Oryza minuta

Introgression line population is effectively used in mapping quantitative trait loci（QTLs）,identifying favorable genes,discovering hidden genetic variation,evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research.In this study,an advanced backcross and consecutive selfing strategy was used to develop introgression lines（ILs）,which derived from an accession of Oryza minuta（accession No.101133） with BBCC genome,as the donor,and an elite indica cultivar IR24（O.sativa）,as the recipient.Introgression segments from O.minuta were screened using 164 polymorphic simple sequence repeat（SSR） markers in the genome of each IL.Introgressed segments carried by 131 ILs covered the whole O.sativa genome.The average number of homozygous O.minuta segments per introgression line was about 9.99.The average length of introgressed segments was approximate 14.78 cM,and about 79.64% of these segments had sizes less than 20 cM.In the genome of each introgression line,the O.minuta chromosomal segments harbored chromosomal fragments of O.sativa ranging from 1.15% to 27.6%,with an overall average of 8.57%.At each locus,the ratio of substitution of O.minuta alleles had a range of 1.5% 25.2%,with an average of 8.3%.Based on the evaluation of the phenotype of these ILs,a wide range of alterations in morphological and yield-related traits were found.After inoculation,ILs 41,11 and 7 showed high resistance to bacterial blight,brown planthopper and whitebacked planthopper,respectively.These O.minuta-O.sativa ILs will serve as genetic materials for identifying and using favorable genes from O.minuta.

Genome-wide prediction for hybrids between parents with distinguished difference on exotic introgressions in Brassica napus

Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis.The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions.We evaluated seed yield,seed yield related traits and seed quality traits of 363 hybrids of Brassica napus (AACC) derived from two parental populations divergent on massive exotic introgression of related species in three environments.The hybrids presented strong heterosis on seed yield,which was much higher than other investigated traits.Five genomic best linear unbiased prediction models considering the exotic introgression and different marker effects (additive,dominance,and epistatic effects) were constructed to test the prediction ability for different traits of the hybrids.The analysis showed that the trait complexity,exotic introgression,genetic relationship between the training set and testing set,training set size,and environments affected the prediction ability.The models with best prediction ability for different traits varied.However,relatively high prediction ability (e.g.,0.728 for seed yield) was also observed when the simplest models were used,excluding the effects of the special exotic introgression and epistasis effect by5-fold cross validation,which would simplify the prediction for the trait with complex architecture for hybrids with exotic introgression.The results provide novel insights and strategies for genome-wide prediction of hybrids between genetically distinct parent groups with exotic introgressions.

Dissection of heterosis for yield and related traits using populations derived from introgression lines in rice

Despite the great success achieved by the exploitation of heterosis in rice,the genetic basis of heterosis is still not well understood.We adopted an advanced-backcross breeding strategy to dissect the genetic basis of heterosis for yield and eight related traits.Four testcross(TC) populations with 228 testcross F1 combinations were developed by crossing57 introgression lines with four types of widely used male sterile lines using a North Carolina II mating design.Analysis of variance indicated that the effects of testcross F1 combinations and their parents were significant or highly significant for most of the traits in both years,and all interaction effects with year were significant for most of the traits.Positive midparent heterosis(HMP) was observed for most traits in the four TC populations in the two years.The relative HMPlevels for most traits varied from highly negative to highly positive.Sixty-two dominant-effect QTL were identified for HMPof the nine traits in the four TC populations in the two years.Of these,22 QTL were also identified for the performance of testcross F1.Most dominant-effect QTL could individually explain more than 10% of the phenotypic variation.Four QTL clusters were observed including the region surrounding the RM9–RM297 region on chromosome 1,the RM110–RM279–RM8–RM5699–RM452 region on chromosome 2,the RM5463 locus on chromosome 6 and the RM1146–RM147 region on chromosome 10.The identified QTL for heterosis provide valuable information for dissecting the genetic basis of heterosis.

Genetic Diversity and Genetic Changes in the Introgression Lines Derived from Oryza sativa L. Mating with O. rufipogon Griff.

The objectives of the present study were to estimate genetic diversity and genetic changes of introgression lines （ILs） which derived from cultivated rice （Oryza sativa L. cv. Xieqingzao B, XB） mating with common wild rice （O. rufipogon Griff., CWR）. The genetic data of 239 ILs were based on a total of 131 polymorphic microsatellite （SSR） markers distributed across the 12 chromosomes of rice. On average, these ILs possessed 77.1 and 14.31% homozygous bands from XB and CWR, respectively. Most of the ILs were clustered together with XB individual, which was revealed by principal coordinate analysis （PCA） and the program STRUCTURE analysis. The result from PCA demonstrated that some intermediate genotypes between XB and CWR were also found. Moreover, there were some genomic sequence changes including parental bands elimination and novel bands emergence in the ILs. The average Nei＇s gene diversity （He） was 0.296, which was higher than that of cultivated rice. It suggested that interspecific hybridization and gene introgression could broaden the base of genetic variation and lay an important foundation for rice genetic improvement. These different genotypic ILs would provide a better experimental system for understanding the evolution of rice species and the mechanism of alien gene introgression.

Genetic Dissection of Low Phosphorus Tolerance Related Traits Using Selected Introgression Lines in Rice

To dissect the genetic basis of low phosphorus tolerance （LPT）, 114 BC2F4 introgression lines （ILs） were developed from Shuhui 527 and Minghui 86 （recurrent parents）, and Yetuozai （donor parent）. The progenies were tested for 11 quantitative traits under three treatments including normal fertilization in normal soil （as control）, normal fertilization in barren soil and low phosphorus stress in barren soil in Langfang, Hebei Province, China. Moreover, the ILs were investigated at the seedling stage using nutrient solution culture method in greenhouse in Beijing, China. A total of 49 main-effect quantitative trait loci （QTLs） underlying yield related traits were identified in Langfang, and their contributions to phenotypic variations ranged from 6.7% to 16.5%. Among them, 25 （51.0%） QTLs had favorable alleles from donor parent. A total of 48 main-effect QTLs were identified for LPT-related traits in Beijing, and their contributions to phenotypic variations ranged from 7.7% to 16.6%. Among them, 21 （43.8%） QTLs had favorable alleles from donor parent. About 79.6% of the QTLs can be detected repeatedly under two or more treatments, especially QTLs associated with spikelet number per panicle, spikelet fertility and 1000-grain weight, displaying consistent phenotypic effects. Among all the detected QTLs, eight QTLs were simultaneously identified under low phosphorus stress across two environments. These results can provide useful information for the genetic dissection of LPT in rice.

QTL underlying iron and zinc toxicity tolerances at seedling stage revealed by two sets of reciprocal introgression populations of rice(Oryza sativa L.)

Iron and zinc are two trace elements that are essential for rice. But they are toxic at higher concentrations, leading to severe rice yield losses especially in acid soils and inland valleys. In this study, two reciprocal introgression line(IL) populations sharing the same parents were used with high-density SNP bin markers to identify QTL tolerant to iron and zinc toxicities. The results indicated that the japonica variety 02,428 had stronger tolerance to iron and zinc toxicities than the indica variety Minghui 63. Nine and ten QTL contributing to iron and zinc toxicity tolerances,respectively, were identified in the two IL populations. The favorable alleles of most QTL came from 02,428. Among them, q FRRDW2, q ZRRDW3, and q FRSDW11 appeared to be independent of genetic background. The region C11S49–C11S60 on chromosome 11 harbored QTL affecting multiple iron and zinc toxicity tolerance-related traits, indicating partial genetic overlap between the two toxicity tolerances. Our results provide essential information and materials for developing excellent rice cultivars with iron and/or zinc tolerance by marker-assisted selection(MAS).

Introgressions from Oryza rufipogon Increase Photosynthetic Efficiency of KMR3 Rice Lines

To understand the wild Oryza genome effect on photosynthesis and its relation to total dry matter accumulation in an elite rice variety, a set of 40 stable introgression lines(ILs) BC_3F_8 derived from a cross of Oryza sativa(KMR3) × Oryza rufipogon(WR120) were grown under well watered conditions. Leaf gas exchange measurements and leaf chlorophyll estimates were conducted at the flowering stage. The results revealed significant variations in net photosynthetic rate(Pn), transpiration rate(E), transpiration efficiency(Pn/E) and carboxylation efficiency(Pn/C_i). Pn showed significant positive correlation with E, stomatal conductance(g_s), Pn/C_i and total canopy dry matter. Specific leaf area and leaf thickness were not significantly correlated with Pn. Thirty-seven out of 40 ILs showed higher Pn than KMR3 [11.28 μmol/(m^2·s)], and 20 ILs showed higher Pn than WR120 [15.08 μmol/(m^2·s)]. The line IL194 showed the highest Pn [21.62 μmol/(m^2·s)] with increased total canopy dry matter followed by lines IL381, IL106, IL363-12, IL198, IL86-18 and IL50, which exhibited Pn above 18.0 μmol/(m^2·s). The ILs with enhanced Pn are a potential source for developing rice varieties and hybrids with higher biomass and yield.

Molecular characterization of LMW-GS genes from a somatic hybrid introgression line Ⅱ-12 between Triticum aestivum and Agropyron elongatum in relation to quick evolution

In order to exploit the evolution and find novel low-molecular-weight glutenin subunit （LMW-GS） for improvement of common wheat quality, thirteen variants from a somatic hybrid introgression line II-12 between Triticum aestivum cv. Jinan 177 （JN177） and Agropyron elongatum were characterized via genomic PCR. Four clones were pseudogenes because they contained an internal stop codon. The remaining nine variants contained intact open reading frames （ORFs）. Sequence alignment indicates that the proteins deduced from the nine ORFs have similar primary structure with LMW-GS cloned from its parents previously. However, they have some unique modifications in the structures. For example, EU292737 contains not only an extra Cys residue in the C-terminal domain but also a long repetitive domain. Both EU 159511 and EU292738 start their first Cys residue in the N-terminal repetitive domain, but not in the N-conserved domain traditionally. These structural alterations may have positive contributions to wheat flour quality. The results of phylogeny showed that most LMW-GS variances from 11-12 were homologous to those from parent JN177 and other wheat lines. The reason for quick evolution of LMW-GS in 11-12 was discussed.

Introgression of Gossypium klotzschianum Genome into Cultivated Cotton,G.hirsutum

Exotic Gossypium germplasm is a rich source of useful agronomic traits for improvement programs of cultivated cotton.Efficient use of genetic variation available in the wild relatives depends

Yield Traits and Associated Marker Segregation in Elite Introgression Lines Derived from O. sativa × O. nivara

Introgression lines(ILs)derived from interspecific crosses are a source of new genetic variability.A total of 55 ILs derived from two crosses Swarna×O.nivara IRGC81848(population A)and Swarna×O.nivara IRGC81832(population B)were characterized for yield and yield-related traits/QTLs.Segregation of 103 simple sequence repeat(SSR)markers associated with yield-related QTLs was studied.Population A showed an average of 12.6%homozygous O.nivara alleles and population B showed 10.6%.Interestingly,three SSR markers,RM223,RM128 and RM517,showed conspicuous pattern of segregation.The distribution of parental alleles at three loci RM223,RM128 and RM517 linked to yield-related traits was unique.These markers flanked to several yield-related QTLs.RM223,flanking to qyld8.3,was heterozygous in almost all the 55 ILs except in IL10-3S and IL131S.RM128 on chromosome 1 and RM517 on chromosome 3 were mutually exclusive in 46 out of 55 ILs.These 46 ILs showed either of the marker allele RM128 or RM517 from O.nivara but not both.IL166S had both RM128and RM517 from O.nivara and the other ILs showed homozygous Swarna allele at RM517 except IL65S.Population structure assigned the 55 ILs to three sub-populations based on their genomic diversity.IL65S,IL166S,IL248S,IL7K and IL250K showed high yields in multi-location trials,and IL248S was released for cultivation as DRRDhan 40.

Characterization of Newly Developed Wheat/Barley Introgression Lines in Respect of Aluminium Tolerance

The Al tolerance of newly developed wheat/barley disomic addition, substitution and translocation lines carry chromosomes of three different barley cultivars was evaluated by comparing the root growth in solution containing 75 μM AlCl3 at pH 4.0 to that of known Al-tolerant and sensitive wheat genotypes. The wheat Asakaze komugi, barley Manas cultivars and their hybrid derivatives were found to have high levels of Al tolerance. The wheat line Mv9kr1, barley cultivar Igri and progenies of the hybrids were sensitive to Al. In most cases, the Al tolerance of the wheat/barley introgression lines derived from Al-sensitive wheat Mv9kr1 and barley Betzes with moderate Al tolerance was similar to that of the wheat parents, but the 2DS.2DL-1HS translocation line of Mv9kr1/Betzes exhibited more intensive root growth, while accumulating less Al than the parental lines. This indicates that either the lack of the distal part of chromosome 2DL or the presence of the distal part of 1HS improved the Al tolerance level.

Molecular Markers Associated with Starch Content and Implications for Sugarcane Introgression Breeding Using Saccharum spontaneum

Introgression with Saceharum spontaneum intended to broaden the genetic base of sugarcane resulted in an increase in desirable genes for broader adapt ability as well as undesirable genes for high starch content. Markers could provide a quick and efficient method of screening parental genotypes for low starch. The objectives of this study were to identify potential markers associated with starch in S. spontaneum population and evaluate their potential for screening for starch content. Data for starch content and （simple sequence repeats） SSR markers were collected from 51 S. spontaneum clones grown in replicated pots. The mixed procedure of statistical analysis system （SAS） was used to determine markers significantly associated with starch. Thirty-nine out of 357 polymorphic markers were significantly （P 〈 0.05） associated with starch content. Eighteen were positively associated and 21 were negatively associated. The presence of a positive marker produced 39% more starch than absence while the absence of a negative marker produced 57% more starch than presence. Selecting parents using negative markers may be more efficient than selecting using positive markers.