Marker assisted accelerated introgression of null allele of kunitz trypsin inhibitor in soybean

Development of kunitz trypsin inhibitor (KTI)-free soybean is crucial for soy-food industry as the heat inactivation employed to inactivate the anti-nutritional factor in regular soybean incurs extra cost and affects protein solubility. In the presented work, a null allele of KTI from PI542044 was introgressed into cultivar ‘JS97-52’ (recurrent parent) through marker assisted backcrossing. Foreground selection in BC₁F₂, BC₂F₂ and BC₃F₂ was carried out using the null allele-specific marker in tandem with SSR marker Satt228, tightly linked with a trypsin inhibitor Ti locus. Background selection in null allele-carrying plants through 106 polymorphic SSR markers across the genome led to the identification of 9 KTI-free lines exhibiting 98.6% average recurrent parent genome content (RPGC) after three backcrosses, which otherwise had required 5–6 backcrosses through conventional method. Introgressed lines (ILs) were free from KTI and yielded at par with recurrent parent. Reduction of 68.8–83.5% in trypsin inhibitor content (TIC) in ILs compared to the recurrent parent (‘JS97-52’) was attributed to the elimination of KTI.     

Recent advances in molecular marker techniques: Insight into QTL mapping,GWAS and genomic selection in plants

Recent advances in sequencing technology have brought several novel platforms for marker development and subsequent genotyping. The high-throughput and cost effective marker techniques have changed the entire scenario of marker applications. The huge genotypic data obtained with next generation sequencing (NGS) also demands analytical tools, statistical advances, and comprehensive understanding to cope with breeding applications. In the present review, we discussed different available marker techniques, their strengths, and limitations. Emphasis was given on software tools, analytical pipelines, workbenches, and online resources available for marker development. Comparison of SNP genotyping involving complexity reduction techniques like GBS, RRL, RAD, and array-based platforms were presented in a view to describe suitability for specific purposes. We found that genotyping by whole genome re-sequencing has great potential, and could be a routine application in the near future with continuously decreasing cost of sequencing. Microsatellites, still a valuable option for breeders, have also advanced with NGS. Here a catalogue of tools for microsatellite evaluation in short sequence reads was provided. The most common applications of molecular marker like QTL mapping, genome-wide association mapping (GWAS), and genomic selection were highlighted. The present review will be helpful for the effective utilization of available resources and for the planning of crop improvement programs employing molecular marker techniques.     

Fusarium wilt of chickpea: physiological specialization, genetics of resistance and resistance gene tagging

Chickpea wilt caused by Fusarium oxysporum f. sp. ciceris is one of the major yield limiting factors in chickpea. The disease causes 10–90% yield losses annually in chickpea. Eight physiological races of the pathogen (0, 1A, 1B/C, 2, 3, 4, 5 and 6) are reported so far whereas additional races are suspected from India. The distribution pattern of these races in different parts of the world indicates regional specificity for their occurrence leading to the perception that F. oxysporum f. sp. ciceris evolved independently in different regions. Pathogen isolates also exhibit differences in disease symptoms. Races 0 and 1B/C cause yellowing syndrome whereas 1A, 2, 3, 4, 5 and 6 lead to wilting syndrome. Genetics of resistance to two races (1B/C and 6) is yet to be determined, however, for other races resistance is governed either by monogenes or oligogenes. The individual genes of oligogenic resistance mechanism delay onset of disease symptoms, a phenomenon called as late wilting. Slow wilting, i.e., slow development of disease after onset of disease symptoms also occurs in reaction to pathogen; however, its genetics are not known. Mapping of wilt resistance genes in chickpea is difficult because of minimal polymorphism; however, it has been facilitated to great extent by the development of sequence tagged microsatellite site (STMS) markers that have revealed significant interspecific and intraspecific polymorphism. Markers linked to six genes governing resistance to six races (0, 1A, 2, 3, 4 and 5) of the pathogen have been identified and their position on chickpea linkage maps elucidated. These genes lie in two separate clusters on two different chickpea linkage groups. While the gene for resistance to race 0 is situated on LG 5 of Winter et al. (Theoretical and Applied Genetics 101:1155–1163, 2000) those governing resistance to races 1A, 2, 3, 4 and 5 spanned a region of 8.2 cM on LG 2. The cluster of five resistance genes was further subdivided into two sub clusters of 2.8 cM and 2.0 cM, respectively. Map-based cloning can be used to isolate the six genes mapped so far; however, the region containing these genes needs additional markers to facilitate their isolation. Cloning of wilt resistance genes is desirable to study their evolution, mechanisms of resistance and their exploitation in wilt resistance breeding and wilt management.     

Widening the gene pool of cultivated lentils through introgression of alien chromatin from wild Lens subspecies

Wild Lens species/subspecies are a potential source for increasing genetic diversity in cultivated lentil. Four intraspecific crosses were attempted between cultivated and wild lentils. Viable hybrids were produced between L. culinaris ssp. culinaris × L. culinaris ssp. orientalis and L. culinaris ssp. culinaris × L. culinaris ssp. odomensis. Normal meiosis and pollen fertility were observed in the first set of crosses, whereas chromosomal abnormalities and reduced pollen fertility were observed in the second set of crosses. These crosses were also studied for some quantitative traits. The range, mean and coefficient of variation were calculated in parents, F₁, F₂ and BC₁ generations to determine the extent of variability generated in the cultivated lentil through introgression of genes from wild lentil. The cultivated lentil × L. culinaris ssp. orientalis crosses showed substantially higher variability for all the traits than crosses involving cultivated lentil ×L. culinaris ssp. odomensis. The results of the present study indicated that these wild subspecies can be exploited for breeding purposes and their variation can easily be utilized to widen the genetic base of the cultivated lentil.     

Genotypic differences in organogenesis from callus of ten triticale lines

Summary Callus was obtained from immature excised embryos of triticale using MS medium supplemented with 3 mg/l 2,4-D and 1 mg/l kinetin. The presence of 2,4-D was essential for continued callus proliferation. Plantlets were induced from the calli by sub-culturing on medium either devoid of auxin or containing 0.1 mg/l 2,4-D. The capacity to produce callus and to form organs and plantlets differed markedly among the genotypes used. Lines also had distinct response to presence and absence of 2,4-D in the regeneration media. The callus of most triticale lines used differentiated into organs more readily on MS medium supplemented with 0.1 mg/l 2,4-D than on medium without growth regulators. Very high frequencies (up to 75%) of plantlet regeneration were observed in several of the triticale lines studied.     

Inheritance of Induced Morphological Mutants in Triticutn monococcum L.

The mode of inheritance of fifteen induced morphological mutants in diploid wheat Triticum monococcum L. was determined. The results showed that earliness, reduced height, uniculm, liguleless branched spike, compact ear, and free-threshing habit of each of these mutants is the result of a single recessive mutation. Red awns and xantha traits are controlled by two recessive genes with duplicate and inhibitory gene interactions, respectively. Some of the early and dwarf mutants were non-allelic. One dwarf GA₃-insensitive mutant with recessive gene action may be a new source. Mutants such as early maturing, dwarf and free threshing habit may be of significance in breeding diploid wheat.     

Discovery of a new gene causing dark green cotyledons and pathway of pigment synthesis in lentil (Lens culinaris Medik)

A new gene is reported which functions as a master gene for synthesis of the pigments determining cotyledon colour in lentil. This gene is different from the two earlier reported genes which are responsible for synthesis of yellow (gene Y) and brown (gene B) pigments. Double recessive homozygous condition of these two genes results into loss of both pigments and, consequently, produces light green cotyledons. The new gene, in contrast, produces dark green cotyledons in recessive condition irrespective of the dominance or recessive state of the Y and B genes. It is hypothesized that the new gene for dark green cotyledon colour (Dg) acts at an earlier stage in the biosynthesis of the two cotyledon-specific pigments, which are derived from a common precursor, whose synthesis is blocked when Dg mutates to its recessive condition. This revised version was published online in August 2006 with corrections to the Cover Date.     

A new gene for resistance in rice to Asian rice gall midge (Orseolia oryzae Wood Mason) biotype 1 population at Raipur, India

The Asian rice gall midge, Orseolia oryzae Wood Mason (Diptera: Cecidomyiidae), is a major pest of rice in several South and South East Asian countries. The maggots feed internally on the growing tips of the tillers and transform them into tubular galls, onion leaf-like structures called ‘silver shoots’ resulting into severe yield loss to the rice crop. We studied the mode of inheritance and allelic relationships of the resistance genes involved in resistant donor Line 9, a sib of a susceptible cultivar ‘Madhuri’. The segregation behaviour of F₁, F₂ and F₃ populations of the cross between Line 9 and susceptible cultivar MW10 confirmed the presence of a single dominant gene for resistance. Tests of allelism with all the known genes giving resistance to this population indicated that Line 9 possessed a new gene which was designated Gm 9 This revised version was published online in July 2006 with corrections to the Cover Date.     

Inheritance of growth vigour and its association with other characters in chickpea

Growth vigour plays an important role in the establishment of a normal crop. The F₂ population of a cross between high‐ and low‐growth vigour varieties of chickpea segregated into 15 high : 1 low growth vigour. The results for recombinant inbred lines and BC1P₂ showed a good fit to the expected 3 : 1 ratio. The results indicated that growth vigour is controlled by two genes with duplicate dominant epistasis. No gene has so far been identified for growth vigour in chickpea. Correlation between growth vigour and other characters showed that high growth vigour had significant negative correlation with days to first flower, days to 50% flowering, days to first pod and days to maturity.