Identification of genomic regions linked to blast (Pyricularia grisea) resistance in pearl millet

Blast disease causes serious economic yield losses in pearl millet. Identification and introgression of genomic regions associated with blast resistance can help to develop resistant cultivars to minimize yield losses incurred from blast outbreaks. In this study, 384 advanced pearl millet genotypes were screened against six blast pathotype-isolates (major pearl millet growing agro-ecologies of India), namely, Pg 45, Pg 118, Pg 138, Pg 186, Pg 204 and Pg 232. Analysis of variance showed significant (P < .001) variation among genotypes for blast reaction (susceptible to resistance). ICMR 08111 and ICMR 10888 genotypes showed resistance to all six blast pathotypes. A genome-wide association study performed with 264,241 single nucleotide polymorphic markers could successfully identify 15 SNPs (P = 1.26 × 10⁻⁷ to 9.22 × 10⁻¹²) underlying the genomic regions governing blast-resistance across five different chromosomes. The SNPs reported had a significant association in at least two of the three models tested (GLM, MLM and Farm CPU). These SNPs can be used in pearl millet-resistant breeding programmes after their function has been validated across different genetic backgrounds.     

Effectiveness of Ethrel as a Male Gametocide in Pearl Millet and its Influence on Ergot

In field and greenhouse experiments Ethrel (2-chloroethyl phosphonic acid) was tested for its male garnetocidal effects on pearl millet (Pennisetum americanum) and its subsequent effects on ergot development. Application of Ethrel at 2000 ppm at late boot or early protogyny was the most effective for inducing male sterility in the hybrid, EJ 104. Female fertility in a male sterile line, however, was not affected by Ethrel treatment. Ethrel at 2030 ppm applied at ihe late boot stage resulted1 in partial paniele exsertion, and reduced plant height anc. panide length. In vitro Ethrel (2000 ppm) completely inhibned pollen germination but did not affect germination of conidia of Claviceps fusiformis, the causal agent of ergot of pearl millet. Ergot resistance or susceptibility in pearl millet lines was not affected., probably because Ethrel could not induce complete male sterility.     

Developing and validating microsatellite markers in elephant grass (<Emphasis Type="Italic">Pennisetum purpureum</Emphasis> S.)

Elephant grass [Pennisetum purpureum S.; syn. Cenchrus purpureus (Schumach.) Morrone] is an important global forage crop and is recognized for high yields of herbage with good nutritive value. It also has high biomass potential to be utilized as a biofuel feedstock. Whereas several previous genetic studies adapted simple sequence repeat (SSR) markers from pearl millet [Pennisetum glaucum (L.) R.Br.] for investigations in elephant grass, the present study developed SSR markers from 3536 DNA sequences derived from 16 elephant grass entries. A total of 3866 SSRs were identified including 1028 monomeric, 2019 dimeric, 735 trimeric, 49 tetrameric, 20 pentameric and 15 hexameric repeat motifs. Three hundred and seven sequences contained more than one repeated motif, and 154 SSRs were present in compound formation. Susequenctly,  four elephant grass and two pearl millet genotypes were chosen to validate 727 SSR markers. Of these, 628 markers produced visually detectable amplification products, including 73 (11.6%) polymorphic ones across all six genotypes. Polymorphism between the four elephant grass genotypes was revealed by 316 (50.6%) markers with diversity index values ranging from 0.75 to 0.38. Dimeric SSRs had the highest polymorphic rate (48.7%). These validated SSR markers had 58.6% (368 of 628) transferability rate to pearl millet. The availability of these polymorphic SSR markers will support advanced genetic studies in P. purpureum and its relatives.     

Development of SCAR and CAPS markers linked to a recessive male sterility gene in lettuce (<Emphasis Type="Italic">Lactuca sativa</Emphasis> L.)

Genetic male sterility (GMS) has been a useful system for the production of hybrid varieties in self-pollinated plants. We obtained a GMS line developed from a spontaneous mutation in lettuce (Lactuca sativa L.). Genetic analysis in our previous study revealed that the sterility was controlled by a recessive gene which was named ms-S. For simple and quick screening of individuals showing male sterility, we attempted molecular mapping of the ms-S locus using an amplified fragment length polymorphism (AFLP) technique. From the examination of 4,096 AFLP primer combinations, 63 AFLP markers were found to be linked to the gene and nine of them were successfully converted into sequence characterized amplified region (SCAR) markers and cleaved amplified polymorphic sequence (CAPS) markers. Linkage analysis indicated that these nine markers were closely linked to the ms-S gene and all were located on the same side of the gene. The minimum genetic distance between the ms-S gene and a marker was 3.1 cM. These results provide additional information for map-based cloning of the ms-S gene and will be of great help for lettuce breeding using GMS to produce F₁ hybrids.     

Linkage mapping and genome analysis in a Saccharum interspecific cross using AFLP, SRAP and TRAP markers

Framework genetic linkage maps of two progenitor species of cultivated sugarcane, Saccharum officinarum ‘La Striped’ (2n = 80) and S. spontaneum ‘SES 147B’ (2n = 64) were constructed using amplified fragment length polymorphism (AFLP), sequence related amplified polymorphism (SRAP), and target region amplification polymorphism (TRAP) markers. The mapping population was comprised of 100 F₁ progeny derived from the interspecific cross. A total of 344 polymorphic markers were generated from the female (S. officinarum) parent, out of which 247 (72%) were single-dose (segregating in a 1:1 ratio) and 33 (9%) were double-dose (segregating in a 3.3:1 ratio) markers. Sixty-four (19%) markers deviated from Mendelian segregation ratios. In the S. spontaneum genome, out of a total of 306 markers, 221 (72%) were single-dose, 43 (14%) were double-dose, and 42 markers (14%) deviated from Mendelian segregation ratios. Linkage maps with Kosambi map distances were constructed using a LOD score ≥5.0 and a recombination threshold of 0.45. In Saccharum officinarum, 146 markers were linked to form 49 linkage groups (LG) spanning 1732 cM whereas, in S. spontaneum, 121 markers were linked to form 45 LG spanning 1491 cM. The estimated genome size of S. officinarum ‘La Striped’ was 2448 cM whereas that of S. spontaneum ‘SES 147B’ was 3232 cM. Based on the two maps, genome coverage was 69% in S. officinarum and 46% in S. spontaneum. The S. officinarum parent ‘La Striped’ behaved like an auto-allopolyploid whereas S. spontaneum ‘SES 147B’ behaved like a true autopolyploid. Although a large disparity exists between the two genomes, the existence of simple duplex markers, which are heterozygous in both parents and segregate 3:1 in the progeny, indicates that pairing and recombination can occur between the two genomes. The study also revealed that, compared with AFLP, the SRAP and TRAP markers appear less effective at generating a large number of genome-wide markers for linkage mapping in sugarcane. However, SRAP and TRAP markers can be useful for QTL mapping because of their ability to target gene-rich regions of the genome, which is a focus of our future research.     

RAPD markers linked with restorer genes for the C-source of cytoplasmic male sterility in rye (Secale cereale L.)

The study was aimed at the identification of random amplified polymorphic DNA markers linked to genes controlling male sterility in rye with the C‐source of sterility‐inducing cytoplasm. Markers of male sterility were distinguished using bulk segregant analysis, carried out on the two F₂ crosses between male sterile and male fertile inbred lines. Screening of polymorphisms revealed by 1000 arbitrary 10‐mer primers allowed the detection of 10 markers in the cross between 711‐cmsC and DS2 lines and seven markers in the cross between 544‐cmsC and Ot0‐20 lines. Five markers were common for the two crosses, which allowed comparative mapping to be performed. Ten markers were mapped on the 4RL chromosome arm where two linked quantitative trait loci (QTL) for male sterility were discovered. Additional QTL of minor effect on male fertility were detected between the two linked markers provisionally assigned to the 6RS chromosome arm. The effectiveness of the marker‐assisted selection (MAS) for male‐sterile genotypes was evaluated.     

Inheritance of sugar and acid contents in the ripe berries of a tetraploid × diploid grape cross population

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a major warm-season cereal, grown primarily for grain production in the arid and semi-arid tropical regions of Asia and Africa. Iron (Fe) and zinc (Zn) deficiencies have been reported to be a food-related primary health problem affecting nearly two billion people worldwide. Improving Fe and Zn densities of staple crops by breeding offers a cost-effective and sustainable solution to reducing micronutrient malnutrition in resource poor communities. An understanding of the genetics of these micronutrients can help to accelerate the breeding process, but little is known about the genetics and heterosis pattern of Fe and Zn densities in pearl millet. In the present study, ten inbred lines and their full diallel crosses were used to study the nature of gene action and heterosis for these micronutrients. The general combining ability (GCA) effects of parents and specific combining ability (SCA) effects of hybrids showed significant differences for both of the micronutrients. However, the predictability ratio (2σ²gca/(2σ²gca + σ²sca)) was around unity both for Fe and Zn densities, implying preponderance of additive gene action. Further, highly significant positive correlation between mid-parent values and hybrid performance, and no correlation between mid-parent values and mid-parent heterosis confirmed again the predominant role of additive gene action for these micronutrients. Barring a few exceptions with one parent, hybrids did not outperform the parents having high Fe and Zn levels. This showed that there would be little opportunity, if any, to exploit heterosis for these mineral micronutrients in pearl millet. In general, high Fe and Zn levels in both of the parental lines would be required to increase the probability of breeding high Fe and Zn hybrids.     

Genetic effects and genetic relationships among <Emphasis Type="Italic">shrunken</Emphasis> (<Emphasis Type="Italic">sh2</Emphasis>) sweet corn lines and F1 hybrids

The objectives of this study were to quantify the components of genetic variance and the genetic effects, and to examine the genetic relationship of inbred lines extracted from various shrunken2 (sh2) breeding populations. Ten diverse inbred lines developed from sh2 genetic background, were crossed in half diallel. Parents and their F1 hybrids were evaluated at three environments. The parents were genotyped using 20 polymorphic simple sequence repeats (SSR). Agronomic and quality traits were analysed by a mixed linear model according to additive-dominance genetic model. Genetic effects were estimated using an adjusted unbiased prediction method. Additive variance was more important than dominance variance in the expression of traits related to ear aspects (husk ratio and percentage of ear filled) and eating quality (flavour and total soluble solids). For agronomic traits, however, dominance variance was more important than additive variance. The additive genetic correlation between flavour and tenderness was strong (r = 0.84, P < 0.01). Flavour, tenderness and kernel colour additive genetic effects were not correlated with yield related traits. Genetic distance (GD), estimated from SSR profiles on the basis of Jaccard’s similarity coefficient varied from 0.10 to 0.77 with an average of 0.56. Cluster analysis classified parents according to their pedigree relationships. In most studied traits, F1 performance was not associated with GD.     

Variations in chlorosis and potential usefulness of alloplasmic Brassica rapa with the cytoplasm of male sterile Brassica juncea

To select superior seed parents for vegetable hybrid seed production, we conducted interspecific crosses between male sterile Brassica juncea (2n = 36, AABB) and eight inbred lines of Brassica rapa (2n = 20, AA). Alloplasmic lines of B. rapa with the cytoplasm of B. juncea were developed from B. juncea × B. rapa hybrids by repeated backcrossing using B. rapa as the recurrent male parent until the BC₃ generation. Seed fertility, male sterility and chlorophyll content were investigated in these plants cultivated under four different temperature conditions (5, 10, 12 and 20°C). At 10°C, the alloplasmic lines of B. rapa with the cytoplasm of B. juncea were male sterile with partly chlorotic leaves. The alloplasmic B. rapa had lower chlorophyll a, chlorophyll b and carotenoid contents than those of the original B. rapa. The leaves recovered from chlorosis when the plants were cultivated at 20°C. An alloplasmic line of B. rapa (A6) is available as a seed parent for vegetable hybrid seed production and contributes seed fertility, slight chlorosis and stable male sterility.     

Fine mapping of <Emphasis Type="Italic">Rf3</Emphasis> and <Emphasis Type="Italic">Rf4</Emphasis> fertility restorer loci of WA-CMS of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) and validation of the developed marker system for identification of restorer lines

The Wild Abortive (WA) system is the major cytoplasmic male sterility (CMS) source for hybrid rice production in indica rice and its fertility restoration is reported to be controlled by two major loci viz. Rf3 on chromosome 1 and Rf4 on chromosome 10. With the availability of the rice genome sequence, an attempt was made to fine map, develop candidate gene based markers for Rf3 and Rf4 and validate the developed marker system in a set of known restorer lines. Using polymorphic markers developed from microsatellite markers and candidate gene based markers from Rf3 and Rf4 loci, local linkage maps were constructed in two mapping populations of ~1,500 F₂ progeny from KRH2 (IR58025A/KMR3R) and DRRH2 (IR68897A/DR714-1-2R) hybrids. QTLs and their interactions for fertility restoration in Rf3 and Rf4 loci were identified. The identified QTL in both mapping populations together explained 66–72 % of the phenotypic variance of the trait suggesting their utility in developing a marker system for identification of fertility restorers for WA-CMS. Sequence comparison of the two candidate genes from the Rf3 and Rf4 regions in male sterile (A) and restorer (R) lines showed 2–3 bp indels and a few substitutions in the Rf3 region and indels of 327 and 106 bp in the Rf4 region respectively. The marker system identified in the present study was validated in 212 restorers and 34 maintainers along with earlier reported markers for fertility restoration of WA-CMS. Together DRCG-RF4-14 and DRCG-RF4-8 for the Rf4 locus and DRRM-RF3-5/DRRM-RF3-10 for the Rf3 locus showed a maximum efficiency of 92 % for identification of restorers.     

Tropospheric ozone pollution reduces the yield of African crops

Northern, Southern and Equatorial Africa have been identified as among the regions most at risk from very high ozone concentrations. Whereas we know that many crop cultivars from Europe, north America and Asia are sensitive to ozone, almost nothing is known about the sensitivity of staple food crops in Africa to the pollutant. In this study cultivars of the African staple food crops, Triticum aestivum (wheat), Eleusine coracana (finger millet), Pennisetum glaucum (pearl millet) and Phaseolus vulgaris (bean) were exposed to an episodic ozone regime in solardomes in order to assess whether African crops are sensitive to ozone pollution. Extensive visible leaf injury due to ozone was shown for many cultivars, indicating high sensitivity to ozone. Reductions in total yield and 1,000-grain weight were found for T. aestivum and P. vulgaris, whereas there was no effect on yield for E. coracana and P. glaucum. There were differences in sensitivity to ozone for different cultivars of an individual crop, indicating that there could be possibilities for either cultivar selection or selective crop breeding to reduce sensitivity of these crops to ozone.     

Mapping of male sterility gene ms10 in chilli pepper (Capsicum annuum L.)

Most of the hybrid seed in chilli are produced manually, but the use of male sterility (MS) can reduce the cost of hybrid seed production. MS‐12, a nuclear male‐sterile (NMS) line developed at Punjab Agricultural University, Ludhiana (India), has been utilized to develop commercial F₁ hybrids. A recessive gene, designated as ms10, governs MS in MS‐12. Due to recessive gene control, development of new NMS lines incorporating ms10 gene is tedious and time‐consuming. We identified SSR markers AVRDC‐PP12 and AVRDC_MD997* linked to the ms10 gene. A total of 558 primer pairs were screened following bulked segregant analysis (BSA). Linkage analysis in 210 F₂ plants indicated that the two SSR markers were linked to the ms10 gene and the marker AVRDC‐PP12 was closest to the gene at 7.2 cM distance. The marker was mapped to chromosome 1 at genome position 175 694 513 to 175 694 644. Until more closely linked markers are developed, the marker AVRDC‐PP12 would facilitate transfer of ms10 gene through marker‐assisted selection (MAS). Fine mapping would lead to cloning of the ms10 gene.     

Differential Competitive Ability and Growth Habit of Pearl Millet and Clusterbean Cultivars in a Mixed Cropping System in the Arid Zone of India

Dryland sustainable agriculture in the arid zone of India depends upon the choice of suitable cultivars for pure and mixed crop stands. Field experiments were conducted for two years to examine the response of two contrasting cultivars each of pearl millet (Pennisetum glaucum) and clusterbean (Cyamopsis tetragonoloba) in pure stands and in mixed pearl millet‐clusterbean stands. The differential response of cultivars of both crops to pure and mixed stands resulted in a significant genotype × cropping system interaction. Reduction in seed yield of both clusterbean cultivars was greater in mixed stands with tall and long duration pearl millet MH 179 than with medium statured and early maturing HHB 67. The degree of reduction was greater in Naveen, the branched clusterbean cultivar, than in RGC 197, the single stemmed cultivar. Mixing of pearl millet HHB 67 with medium duration clusterbean cultivar Naveen produced maximum pearl millet equivalent total yield. Higher land equivalent ratios (LERs) were also observed when clusterbean cultivars were mixed with early maturing and short statured pearl millet HHB 67.     

谷子显性雄性不育基因Msch的AFLP标记

利用雄性不育是实现谷子杂种优势利用最经济、有效的途径之一.为了寻找与不育基因Msch紧密连锁的分子标记,提高不育系的选育效率,本研究构建了Msch不育/可育近等基因系(NILs),通过对400对AFLP引物组合进行筛选,找到了与不育基因紧密连锁的两个AFLP标记(P17/M37224和P35/M52208),与不育基因的遗传距离分别是2.1 cM和1.4 cM,而且位于不育基因的同一侧,标记间相距0.7 cM.这两个AFLP标记可有效用于分子标记辅助选择育种.     

Identification of DNA markers linked to an induced mutated gene conferring resistance to powdery mildew in pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.)

We have recently induced two powdery mildew (Erysiphe pisi Syd) resistant mutants in Pisum sativum L. via ethylnitrosourea (ENU) mutagenesis. Both mutations (er1mut1 and er1mut2) affected the same locus er1 that determines most of the identified natural sources of powdery mildew resistance (PMR) in this crop. The mutated gene er1mut2 was mapped to a linkage group of 16 DNA markers combining three main strategies: near isogenic lines (NILs) analysis, bulked segregant analysis and genetic mapping of randomly identified polymorphic markers, together with three DNA-markers techniques: ISSR, RAPDs and AFLPs. Markers located closer to the PMR locus, OPO06_1100y (0.5 cM), OPT06₄₈₀ (3.3 cM) and AGG/CAA₁₂₅ (5.5 cM), were cloned and converted into SCAR markers. Markers AH1R₈₅₀ and AHR_920y were found to be allelic and converted into the co-dominant marker ScAH1 (16.3 cM). Two previously known DNA markers, ScOPE16₁₆₀₀ and A5_420y, were mapped at 9.6 and 23.0 cM from the PMR locus, respectively. The novel markers identified in this study are currently being transferred to a new F2 mapping population derived from a cross between the induced PMR mutant line F(er1mut2) and a more genetically distant susceptible line of Pisum sativum var. arvense.     

Identification of quantitative trait loci for bruchid (<Emphasis Type="Italic">Callosobruchus maculatus</Emphasis>) resistance in black gram [<Emphasis Type="Italic">Vigna mungo</Emphasis> (L.) Hepper]

An inter-subspecific mapping population was generated by crossing V. mungo var. mungo (cv. TU 94-2, bruchid susceptible) and V. mungo var. silvestris (bruchid resistant). About 37.8% of the bruchid completed their lifecycle on seeds of V. mungo var. silvestris compared with 100% on the susceptible variety TU 94-2. The total developmental period of C. maculatus on Vigna mungo var. silvestris was considerably extended (88 days as compared with 34 days on TU 94-2). A genetic linkage map constructed using recombinant inbred lines (RILs) in F₉ generation with 428 markers [86 random amplified polymorphic DNA (RAPD), 47 simple sequence repeat (SSR), 41 inter-SSR (ISSR), 254 amplified fragment length polymorphism (AFLP)] was used for QTL detection. One hundred four individuals were used for detection of QTLs associated with bruchid resistance. The RILs exhibited a high level of variation in percentage adult emergence (0–100%) and developmental period (0–105 days). Two QTLs, Cmrae1.1 and Cmrae1.2, were identified for percentage adult emergence, on linkage group (LG) 3 and 4, respectively. For developmental period, six QTLs were identified, with two QTLs (Cmrdp1.1 and Cmrdp1.2) on LG 1, three QTLs (Cmrdp1.3, Cmrdp1.4, and Cmrdp1.5) on LG 2, and one QTL (Cmrdp1.6) on LG 10.     

Morphological,cytological and reproductive characterization of tri-species hybrids (GOS) between <Emphasis Type="Italic">Pennisetum glaucum</Emphasis>, <Emphasis Type="Italic">P. orientale</Emphasis> and <Emphasis Type="Italic">P. squamulatum</Emphasis>

New tri-species hybrids (GOS) in the genus Pennisetum involving the cultivated species pearl millet (P. glaucum L.) and two wild species, viz. P. squamulatum Fresen and P. orientale L. C. Rich, are reported. Six hybrid plants were recovered after crossing a backcross hybrid (2n = 3x = 23, GGO) between P. glaucum (2n = 2x = 14, GG) and P. orientale (2n = 2x = 18, OO) with F₁s (2n = 6x = 42, GGSSSS) between P. glaucum (2n = 4x = 28, GGGG) and P. squamulatum (2n = 8x = 56, SSSSSSSS). The hybrids were perennial, morphologically intermediate to their parents, and represented characters from the three contributing species. The hybrids contained 2n = 44 chromosomes (GGGSSO) representing 21, 14 and nine chromosomes from P. glaucum, P. squamulatum and P. orientale, respectively. Meiotic and flow-cytometric analysis suggested origin of these hybrids from unreduced female and reduced male gametes. Average chromosome configuration (8.42_I + 14.32_II + 1.62_III + 0.52_IV) at Meiosis showed limited inter-genomic pairing indicating absence of significant homology between the three genomes. The hybrids were male sterile (except one) and highly aposporous. P. orientale was identified to induce apospory in hybrid background with P. glaucum at diploid and above levels, though it was quantitatively affected by genomic doses from sexual parent. A case of inducible and recurrent apospory is presented whereby a transition from Polygonum-type sexual embryo-sacs to Panicum-type aposporous embryo-sacs was observed in diploid interspecific hybrids. Results supported independent origin and partitioning of the three apomixis-components (apomeiosis, parthenogenesis, and functional endosperm development), reported for the first time in Pennisetum. Potential utilization of GOS hybrids in understanding genome interactions involved in complex traits, such as perenniality and apomixis, is discussed.     

Allele mining and haplotype discovery in barley candidate genes for drought tolerance

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.     

Identification of RAPD and SCAR markers linked to northern leaf blight resistance in waxy corn (Zea mays var. ceratina)

Exserohilum turcicum causes northern corn leaf blight (NCLB), an important disease occurring in maize producing areas throughout the world. Currently, the development of cultivars resistant to E. turcicum seems to be the most efficient method to control NCLB damage. Marker-assisted selection (MAS) enables breeders to improve selection efficiency. The objective of this work was to identify random amplified polymorphic DNA (RAPD) and sequence characterized amplified region (SCAR) markers associated with NCLB resistance. Bulked segregant analysis (BSA) was used to search for RAPD markers linked to NCLB resistance genes, using F₂ segregating population obtained by crossing a susceptible inbred ‘209W’ line with a resistant inbred ‘241W’ line. Two hundred and twenty-two decamer primers were screened to identify four RAPD markers: OPA07₅₂₁, OPA16₄₅₇, OPB09₅₂₀, and OPE20₅₃₆ linked to NCLB resistance phenotype. These markers were converted into dominant SCAR markers: SCA07₄₉₆, SCA16₄₂₀, SCB09₄₆₄, and SCE20₄₂₉, respectively. The RAPD and SCAR markers were developed successfully to identify NCLB resistant genotypes in segregating progenies carrying NCLB resistant traits. Thus, the markers identified in this study should be applicable for MAS for the NCLB resistance in waxy corn breeding programs.