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

Integrating phenotypic and molecular profiling for selection of promising advanced breeding lines for blast resistance in rice (Oryza sativa L.)

BACKGROUND

Rice is susceptible to several major and minor diseases, with blast disease caused by Magnaporthe oryzae being a significant constraint, leading to substantial economic losses worldwide. Exploiting genetic resistance in cultivars is a preferred strategy for managing this disease, offering an alternative to chemical control.

METHODS AND RESULTS

The objective of this study was to identify advanced breeding lines (ABLs) with blast resistance, superior yield, and good grain quality using Marker-Assisted Selection (MAS). Leaf blast resistance screening revealed that 25 ABLs exhibited moderate resistance. Molecular analysis with 10 polymorphic markers linked to blast resistance genes (Pi1, Pi2, Pi9, Pi37, Pi38, Pi39, Pi54, Pita, Pitp, and Piz5) identified the highest number of positive alleles (8) in MTU1061, IR36, and SVGP-26. Additionally, seven ABLs (SVGP-1, SVGP-14, SVGP-23, SVGP-37, SVGP-38, SVGP-39, and SVGP-48) showed co-segregation of markers with blast resistance. Genetic diversity analysis revealed significant variability among the genotypes, indicating diverse genetic backgrounds. Based on their yield performance, quality traits, and resistance to blast, five parents (NLR 34449, NLR 40024, MTU 1061, MTU 3626, and IR 36) and five ABLs (SVGP-13, SVGP-16, SVGP-40, SVGP-47, and SVGP-32) were selected for further yield trials.

CONCLUSION

The study identified high-yielding, blast-resistant lines with good grain quality and diverse genetic backgrounds as promising donor sources for improving blast resistance in rice breeding programs. These findings enhance the genetic base for developing resistant rice cultivars with improved agronomic traits.

Allelic Diversity and Development of Breeder-Friendly Marker Specific to floury2 Gene Regulating the Accumulation of α-Zeins and Essential Amino Acids in Maize Kernel

Maize zeins lack essential amino acids, such as methionine, lysine, and tryptophan. The floury2 (fl2) mutation reduces zein synthesis and increases methionine and lysine content in kernels. In this study, fl2 gene (1612 bp) was sequenced in eight wild-type and two mutant inbreds and detected 218 SNPs and 18 InDels. Transversion of C to T at 343 bp position caused the substitution of alanine by valine in the fl2 mutant. A PCR-based marker (FL-SNP-CT) was developed, which distinguished the favorable mutant fl2 allele (T) from the wild-type (C) Fl2 allele. Gene-based diversity analysis using seven gene-based InDel markers grouped 48 inbred lines into three major clusters, with an average genetic dissimilarity coefficient of 0.534. The average major allele frequency, gene diversity, heterozygosity, and polymorphism information content of the InDel markers were 0.701, 0.392, 0.039, and 0.318, respectively. Haplotype analysis revealed 29 haplotypes of fl2 gene among these 48 inbreds. Amino acid substitution (Ala-Val) at the signal peptide cleavage site produced unprocessed 24-kDa mutant protein instead of 22-kDa zein found in normal genotype. Eight paralogues of fl2 detected in the study showed variation in exon lengths (616-1170 bp) and translation lengths (135-267 amino acids). Orthologue analysis among 15 accessions of Sorghum bicolor and two accessions of Saccharum spontaneum revealed a single exon in fl2 gene, ranging from 267 to 810 bp. The study elucidated the molecular basis of fl2 mutation and reported a breeder-friendly marker for molecular breeding programs. This is the first study to characterize fl2 gene in a set of subtropically adapted inbreds.

Genetic enhancement of reproductive stage drought tolerance in RPHR-1005R and derivative rice hybrids through marker-assisted backcross breeding in rice (Oryza sativa L.)

BACKGROUND

Drought stress is considered as one of the major production constraints in rice. RPHR-1005R is a restorer line (R-Line) with a popular, medium-slender grain type, and is the male parent of the popular Indian rice hybrid, DRR-H3. However, both the hybrid and its restorer are highly vulnerable to the drought stress, which limits the adoption of the hybrid. Therefore, the selection of the restorer line RPHR-1005R has been made with the objective of enhancing drought tolerance.

METHODS AND RESULTS

In this study, we have introgressed a major QTL for grain yield under drought (qDTY 1.1) from Nagina22 through a marker-assisted backcross breeding (MABB) strategy. PCR based SSR markers linked to grain yield under drought (qDTY1.1 - RM431, RM11943), fertility restorer genes (Rf3-DRRM-Rf3-10, Rf4-RM6100) and wide compatibility (S5n allele) were deployed for foreground selection. At BC2F1, a single plant (RPHR6339-4-16-14) with target QTL in heterozygous condition and with the highest recurrent parent genome recovery (85.41%) and phenotypically like RPHR-1005R was identified and selfed to generate BC2F2. Fifty-eight homozygous lines were advanced to BC2F4 and six promising restorer lines and a hybrid combination (APMS6A/RPHR6339-4-16-14-3) were identified.

CONCLUSIONS

In summary, the six improved restorer lines could be employed for developing heterotic hybrids possessing reproductive stage drought tolerance. The hybrid combination (APMS6A/RPHR6339-4-16-14-3) was estimated to ensure stable yields in drought-prone irrigated lowlands as well as in directly seeded aerobic and upland areas of India.

Enhancement of nutritional quality in maize kernel through marker-assisted breeding for vte4, crtRB1, and opaque2 genes

Traditional maize is poor in vitamin-E [α-tocopherol (α-T): 6-8 ppm], vitamin-A [provitamin-A (proA): 1-2ppm], lysine (0.150-0.2-50%), and tryptophan (0.030-0.040%). Here, we combined favourable alleles of vte4, crtRB1, and opaque2 (o2) genes in the parents of maize hybrids, viz., APQH-10 (PMI-PV-9 × PMI-PV-14) and APQH-11 (PMI-PV-9 × PMI-PV-15) using molecular breeding. Gene-specific markers were successfully used to select vte4, crtRB1, and o2 in BC1F1, BC2F1, and BC2F2 generations. Simple sequence repeats (104-109) were used for background selection, leading to an average recovery of 94% recurrent parent genome. The introgressed inbreds possessed significantly higher α-T: 18.38 ppm, α-/γ-tocopherol (α-/γ-T: 52%), and α-/total tocopherol (α-/TT: 32%) compared to original inbreds (α-T: 8.17 ppm, α-/γ-T: 25%, α-/TT: 18%). These newly derived inbreds also possessed higher β-carotene (BC: 8.91 ppm), β-cryptoxanthin (BCX: 1.27 ppm), proA (9.54 ppm), lysine (0.348%), and tryptophan (0.082%) compared to traditional maize inbreds. The reconstituted hybrids recorded higher α-T (2.1-fold), α-/γ-T (1.9-fold), and α-/TT (1.6-fold) over the original hybrids. These reconstituted hybrids were also rich in BC (5.7-fold), BCX (3.3-fold), proA (5.3-fold), lysine (1.9-fold), and tryptophan (2.0-fold) over the traditional hybrids. The reconstituted hybrids had similar grain yield and phenotypic characteristics to original versions. These multinutrient-rich maize hybrids hold great potential to alleviate malnutrition in sustainable and cost-effective manner.

Molecular and Morphological Characterization of Introgression Lines with Resistance to Bacterial Leaf Blight and Blast in Rice

The present study evaluates marker assisted forward breeding (MAFB)-derived disease resistant introgression lines (ILs) which do not have the targeted resistance genes for bacterial blight (xa5 + xa13 + Xa21) and blast (Pi2 + Pi9 + Pi54). The ILs were derived in the background of two elite rice cultivars, Krishna Hamsa [Recurrent Parent 1 (RP1)] and WGL 14 (RP2), involving multi-parent inter-crossing. Molecular characterization with gene specific markers for seven reported resistance genes each for bacterial blight (Xa33, Xa38, xa23, Xa4, xa8, Xa27 and Xa41) and blast (Pi1, Pi20, Pi38, Pib, Pitp, Pizt and Pi40) revealed the presence of xa8 and Xa38, in addition to the targeted xa5, xa13 and Xa21 for bacterial blight resistance and Pi1, Pi38, Pi40, Pi20, Pib and Pipt, in addition to the targeted Pi9 and Pi54, for blast resistance in various combinations. A maximum of nine resistance genes xa5 + Xa21 + Pi54 + xa8 + Pipt + Pi38 + Pi1 + Pi20 + Pib was observed in RP1-IL 19030 followed by eight genes xa5 + xa13 + Xa21 + xa8 + Pi9 + Pipt + Pi1 + Pi20 in two RP2-ILs, 19344 and 19347. ANOVA revealed the presence of significant variability for all the yield traits except "days to 50% flowering" (DFF). Box plots depicted the seasonal differences in the phenotypic expression of the yield traits. There was significant positive association of grain yield with days to flowering, tiller number and panicle number. Thousand grain weight is also significantly and positively correlated with grain yield. On the contrary, grain yield showed a significantly negative association with plant height. Multi-parent selective inter-crossing in the present study not only led to the development of high yielding disease resistant ILs but also enhanced recovery of the recurrent parent via selection for essential morphological features. More than 90.0% genetic similarity in the ILs based on SNP-based background selection demonstrated the success of multi-parent selective intercrossing in the development of disease resistant NILs.