Novel quantitative trait loci for yield and yield related traits identified in Basmati rice (Oryza sativa)

Increasing crop productivity is one of the prime goals of crop breeding research. Rice grain yield is a complex quantitative trait governed by polygenes. Although several QTLs governing grain yield traits have been reported and limited attempts have been made to map QTLs for grain yield parameters in Basmati rice. A population from the cross Sonasal and Pusa Basmati 1121 comprising 352 RILs was generated through the single seed descent method. A total of 12 QTLs governing yield and yield-related traits were mapped on six chromosomes, namely, 1, 2, 3, 7, 8 and 9, of which five QTLs were novel. We identified a novel and robust epistatic QTL (qPH1.1 and qPL1.1) governing plant height and panicle length, flanked by the markers RM5336-RM1 on chromosome 1. The gene encoding brassinosteroid insensitive 1-associated receptor kinase 1 precursor is the putative candidate gene underlying this epistatic QTL. Another novel QTL, qNT3.1, governing tiller number was bracketed to a region of .77 Mb between the markers RM15247 and RM15281 on chromosome 3. Of the 57 annotated gene models, Os03g0437600 encoding alpha/beta-fold hydrolase, a homologous to AtKai2 is a putative candidate gene underlying the novel QTL qNT3.1. The other QTLs such as qDFF1.1 governing days to 50% flowering co-localizes with the gene Ghd7, QTL for plant height qPH1.2 co-localizes with the gene sd1, the QTLs for panicle length co-localizes with FUWA and DEP2, the QTL for tiller number co-localizes with OsRLCK57 and QTLs for thousand-grain weight co-localize with the major gene GS3. The QTLs identified in the current study can be effectively used in marker-assisted selection for developing Basmati rice varieties with a higher yield.     

Genetic analysis and identification of SSR marker linked to Phomopsis blight resistance in eggplant (Solanum melongena L.)

The present investigation was carried out to decipher inheritance of resistance and to identify linked SSR markers for Phomopsis blight resistance in eggplant. An F₂ population comprising 161 plants was developed from the cross of Pusa Kranti and BR-40-7. Genetic analysis was carried out using Chi square test. Artificial inoculation of fruits was carried out using pin prick method, and scoring was done as per the standard scoring scale. The F₂ plants segregated into 92 susceptible (77—highly susceptible, 15—susceptible): 69 resistant (17—highly resistant, 27—resistant, 25—moderately resistant) suggesting complimentary epistasis with ratio of 9:7. To identify the putatively linked markers to resistance gene, parental polymorphic markers were subjected to bulk segregant analysis (BSA), and two markers (emk03O04 and emf11A03) could differentiate resistant and susceptible bulk and co-segregated with resistance gene. The genetic distance between the identified markers was found to be 18.12 cM using QTL IciMapping V3.2 software depicting two new QTLs on chromosome number 6. The identified QTLs have great significant importance in marker assisted breeding programme.     

Cyto-morphological evidence for segmental allopolyploid origin of Teasle gourd (<Emphasis Type="Italic">Momordica subangulata</Emphasis> subsp. <Emphasis Type="Italic">renigera</Emphasis>)

Teasle gourd [Momordica subangulata Blume subsp. renigera (G. Don) de Wilde, 2n = 56] exhibits morphological characters found in both M. dioica (2n = 28) and M. cochinchinensis (2n = 28). Morphological analysis of M. subangulata subsp. renigera suggests an allopolyploid origin. We present evidence elucidating the genomic relationships between M. dioica, M. cochinchinensis and M. subangulata subsp. renigera. A triploid M. dioica × M. subangulata subsp. renigera hybrid had an average of 12.76 bivalents, 13.84 univalents and 0.88 trivalents at metaphase I, while the M. cochinchinensis × M. subangulata subsp. renigera hybrid had an average of 13.08 bivalents, 12.96 univalents and 0.96 trivalents. F₁ hybrids of the two diploid species (M. dioica × M. cochinchinensis) showed an average of 9.12 bivalents and 9.76 univalents, suggesting that the genomes of these species are only partially homologous. A higher number of bivalents in the triploid hybrids suggests that M. subangulata subsp. renigera is a segmental allopolyploid of M. dioica and M. cochinchinensis and that its genomes have diverged from the parental genomes.     

Association of fruit traits and aril browning in pomegranate (<Emphasis Type="Italic">Punica granatum</Emphasis> L.)

Pomegranate cultivation is one of the most attractive farming enterprises in the Indian arid tropics. However, the quality of the fruit is often severely affected by a physiological disorder called ‘aril browning’ in which a part or all the arils show discolouration (browning) and such fruits are unfit for consumption. This has become a serious concern to consumers, growers and researchers in the recent times. In order to understand the genotypic variation for aril browning and its association with other fruit traits, 158 progenies obtained by selfing two pomegranate multiple hybrids viz., {(‘Ganesh’ × ‘Kabul’) × ‘Yercaud’} × {(‘Ganesh’ × ‘Gulsha Rose Pink’)-F₂} and {(‘Yercaud’ × ‘Jyothi’) × (‘Ganesh’ × ‘Gulsha Rose Pink’)-F₂} × {(‘Ganesh’ × ‘Kabul’) × ‘Yercaud’} were studied. Because of heterozygous nature of the crop and diverse genetic base of parents, a wide array of recombinants were produced which were scored for aril browning, fruit skin colour, aril colour, total soluble solids (TSS) and seed mellowness. Results of Spearman’s correlation analysis revealed that aril browning is inversely related with aril colour (r = −0.41). A statistical model constructed to study the reasons for the observed variation in aril browning showed that about 82.9% of it was accounted collectively by skin colour, aril colour, TSS and seed mellowness. Further, a refined model represented by Y (aril browning severity) = 0.78 − 0.52 X₁ (aril colour) + 0.23 X₂ (TSS) was found to contribute to 73.5% of the observed variability in aril browning with least error in prediction. Analysis of data further showed that every unit increase in intensity of aril colour amounted to decrease in severity of aril browning by 0.52 units. However, for every unit increase in TSS there was an increase of 0.23 units in severity of aril browning. Thus, with the increase in intensity of aril colour there was a reduction in severity of aril browning while with raise in TSS, aril browning incidence was higher, an association often not favourable in selection of desirable genotypes. The results of the present study suggested that while developing varieties free from aril browning it is important to strike a balance between aril colour and TSS level.     

Genetics of resistance in <Emphasis Type="Italic">Luffa cylindrica</Emphasis> Roem. against <Emphasis Type="Italic">Tomato leaf curl New Delhi virus</Emphasis>

Sponge gourd is a popular vegetable grown throughout India. Tomato leaf curl New Delhi virus, the causal virus of tomato leaf curl disease, has recently been reported to be associated with sponge gourd, causing up to 100% crop loss under epidemic conditions. We have collected 30 genotypically diverse genotypes of sponge gourd from different parts of India, screened these for resistance under natural epiphytotic conditions, and then confirmed the results through challenge inoculation with a purified strain of the virus under insect-proof greenhouse conditions. The minimum vulnerability index was recorded in genotype DSG-6 (3.33), followed by DSG 7 (6.0) under the challenge (whitefly-populated) inoculation conditions. Two susceptible genotypes (‘Pusa Sneha’ and NSG-1-11), both possessing desirable fruit characters, were crossed with the two most promising resistant lines (DSG-6 and DSG-7) and the disease reaction of segregating and backcross generations studied through challenge inoculation with a purified strain of virus under insect-proof greenhouse conditions. A chi-square (χ²) test of frequency distribution based on the vulnerability index of the F₂ progenies of the two resistant × susceptible crosses revealed monogenic dominant Mendelian ratio 3(R):1(S) to be the best fit in all crosses. This monogenic dominant model was further confirmed by the 1(R):1(S) ratio found to be best fit for the test cross with the susceptible parent. These results reveal that resistance to Tomato leaf curl New Delhi virus associated with yellow mosaic disease of sponge gourd is controlled by a single dominant gene in the genetic background of the resistant parents (DSG-6 and DSG-7) and that these two lines can be effectively utilized for the development of high-yielding and yellow mosaic disease-resistant varieties/hybrids of sponge gourd. This is the first conclusive identification of a resistant source and the inheritance of resistance against Tomato leaf curl New Delhi virus in sponge gourd.     

Genetic Advances in Adapting Rice to a Rapidly Changing Climate

Rice, with its wide geographic distribution extending from 50°N to 35°S, is expected to be the most vulnerable cultivated crop to future changing climates. Among the different abiotic stresses, extreme temperatures coinciding with critical developmental stages, increasingly frequent floods and drought spells, and worsening sea water inundation are some of the major threats to sustainable rice productivity. Following the successful implementation of molecular marker‐assisted backcrossing to introgress large‐effect QTL for submergence tolerance in rice mega varieties, rice breeding for drought, salinity and, recently, heat tolerance is employing the same approach. Although tolerance for combined submergence and salinity has been achieved, developing rice varieties with multiple tolerance for other abiotic and biotic stresses and finding the appropriate agronomic package to exploit their performance remain a challenge. The major bottleneck is the lack of unidentified large‐effect QTL for other abiotic stresses that are strongly influenced by genotype × environment (G × E) interaction. Rapid advances in the use of molecular tools, including a plethora of SNP markers, are expected to facilitate the development of major abiotic stress‐tolerant rice. In response to the actual farmer field situation, progress achieved in understanding and developing independent abiotic stress tolerance is being exploited to combine tolerances (for example, heat and drought; salinity and submergence) to address emerging environmental problems across a wide range of rice ecosystems.     

Genetic mapping and QTL analysis for sugar yield-related traits in sugarcane

Genetic improvement of sugar content in sugarcane would benefit from the availability of sufficient DNA markers and a genetic map. Genetic linkage maps were constructed to identify quantitative trait loci (QTLs) for seedling brix (SB), brix (B), sucrose percent in juice (SUC), stalk number (SN), stalk length (SL), stalk diameter (SD), internodes (INT), number of green leaves (NGL), at three crop cycles across seven environments in a segregating population with 207 individuals derived from a bi-parental cross of sugarcane elite cultivars. Linkage analysis led to the construction of eight linkage groups (LGs) for Co86011 and sixteen LGs for CoH70. The combined length of the two linkage maps was 2606.77 cM distributed over 24 LGs. 31 QTLs were identified: 2 for SB, 7 for B, 6 for SUC, 4 for SN, 1 for SL, 3 for SD, 6 for INT and 2 for NGL at LOD scores ranging from 2.69 to 4.75. 7 QTLs (22 %) had stable effect across crop year and locations. Markers from parents were found to be associated with both positive and negative effect on all of the traits analyzed. The most important QTLs intervals identified in this study using single-dose marker, were qB2, qSUC2, qINT2 and qB2, qSUC2, qSL2, qINT2 located between SSR markers UGSM31₅₄₈ and UGSM31₆₄₉. These QTLs could be put into use in marker assisted breeding.     

Maternal inheritance of male sterility in the progeny of a natural hybrid between Cajanus lineatus and C. cajan

Adoption of pigeonpea hybrids in central and southern India is showing high impact with on‐farm yield advantages of >30%. The hybrid pigeonpea technology, the first in any legume crop, is based on a cytoplasmic‐nuclear male‐sterility (CMS) system. For a long‐term sustainability of hybrid programme, it is imperative that both nuclear diversity and cytoplasmic diversity are maintained among hybrid parents. In this context, a continuous search for new CMS‐inducing cytoplasms is necessary. This paper reports detection of maternal inheritance of male sterility in the progeny derived from a natural hybrid between a wild relative [Cajanus lineatus (W. & A.) Maesen comb. nov.] of pigeonpea and an unknown pigeonpea [Cajanus cajan (L.) Millsp.] genotype. In the present study, the male sterility was maintained up to BC₇F₁ generation by an advanced breeding pigeonpea line ICPL 99044. This male sterility inducing cytoplasm of C. lineatus was tagged as A₆. In future, this CMS genetic stock can be used to develop a range of new pigeonpea hybrids with high yield and adaptation.     

Genetics of resistance to Sesamia inferens infestation and its correlation with yield in maize

Sesamia inferens (Walker) causes 25.7–78.9% losses in maize production in South and South‐East Asia. The genetic basis of host plant resistance is the prerequisite for resistance breeding. Twenty‐four populations derived from S. inferens resistant × susceptible inbreds were used to study the genetic regulation of resistance to S. inferens in maize, to determine the importance of genetic effects through generation mean analysis (GMA) and to understand correlation between resistance and yield. Resistant and susceptible inbreds differed significantly in leaf and stem injury ratings (LSIR), a measure of host plant resistance. Mean LSIR range among resistant and susceptible parents was 2.15–2.55 and 7.83–8.22, respectively. The broad‐sense heritability ranged from 0.40 to 0.71, and the mean number of effective factors ranged from 1.9 to 2.6. The resistance against S. inferens was largely governed by additive × additive (i), followed by dominance (d) and additive (a) gene effects. Significant negative correlation (?0.27 to ?0.96) was observed between LSIR and yield. The findings suggest reciprocal recurrent selection for development of new inbreds with resistance followed by their involvement in hybrid development to exploit additive and non‐additive gene effects/variance.