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Our tropical fruits are vulnerable to climate change. Already, the Australian fruit industry has seen large-scale losses of young fruit trees, or seasons where fruit develops poorly. For millennia, farmers have bred grains, fruit and vegetable varieties to get larger harvests and plants better able to tolerate different climates. [Extracted from the article]

Bacterial blight (BB), caused by Xanthomonas oryzaepv. oryzae(Xoo), is a serious constraint to basmati rice production. The increasingly evident outbreaks of BB in recent years necessitate an immediate search for ecology-conscious, cost-effective and durable management strategy. Given the context, this investigation aimed to generate knowledge about the haplotypic and pathogenic variability of Xoopopulation severely affecting Pusa Rice Hybrid 10 (PRH-10), world’s first superfine aromatic basmati hybrid. Seven haplotypes were detected from the experimental field applying two PCR-based assays, i.e. repetitive sequence-based polymerase chain reaction and insertion sequence based PCR. The experimental results revealed greater genetic heterogeneity in the Xoopopulation with high value of total haplotypic diversity (HT= 0.79). In addition, based on the virulence assay, the genetic heterogeneity corresponded to the presence of four pathotypes. Importantly, the substantial line × strain interactions was significant (p≤ 0.01), which confirmed the host specificity in the system. In parallel, it was noted that most of the key resistance genes except Xa21, deployed in the rice breeding program at International Rice Research Institute were overcome by the Xoostrains, thus underscoring the relevance of this gene in resistance breeding. Therefore, incorporating Xa21alone, or in combination with xa13or xa5into the parental lines, using various modern genomics-assisted approaches might be the potential fast-track strategy to breed PRH-10 with remarkably enhanced BB resistance. The present investigation provides a molecular framework for future epidemiological studies and is likely to assist rice breeders to expedite basmati rice improvement.

Pigeonpea production is severely constrained by wilt disease caused by Fusarium udum. In the current study, we discover the putative genomic regions that control resistance response to variant 2 of fusarium wilt using association mapping approach. The association panel comprised of 89 diverse pigeonpea genotypes including seven varieties, three landraces and 79 germplasm lines. The panel was screened rigorously for 3 consecutive years (2013–14, 2014–15 and 2015–2016) against variant 2 in a wilt-sick field. A total of 65 pigeonpea specific hypervariable SSR markers (HASSRs) were screened representing seven linkage groups and 29 scaffolds of the pigeonpea genome. A total of 181 alleles were detected, with average values of gene diversity and polymorphism information content (PIC) of 0.55 and 0.47, respectively. Further analysis using model based (STRUCTURE) and distance based (clustering) approaches separated the entire pigeonpea collection into two distinct subgroups (K = 2). The marker trait associations (MTAs) were established based on three-year wilt incidence data and SSR dataset using a unified mixed linear model. Consequently, six SSR markers were identified, which were significantly associated with wilt resistance and explained up to 6% phenotypic variance (PV) across the years. Among these SSRs, HASSR18 was found to be the most stable and significant, accounting for 5–6% PV across the years. To the best of our knowledge, this is the first report of identification of favourable alleles for resistance to variant 2 of Fusarium udumin pigeonpea using association mapping. The SSR markers identified here will greatly facilitate marker assisted resistance breeding against fusarium wilt in pigeonpea.

The availability of stable cytoplasmic male sterile (CMS or A) lines coupled with a robust restoration system (R lines) is an essential prerequisite for efficient hybrid breeding. CMS-enabled hybrid technology holds immense potential to enhance the long-stagnant productivity of pigeonpea. In the present investigation, cytoplasmic substitutions were made in the nuclear backgrounds of early-maturing pigeonpea varieties or lines. Three new CMS lines (ICPL 88039A, Pusa 992A, and DPP 3-2A) resulted from genetic crosses involving cytoplasmic donors from A2(GT 288A) and A4(ICPA 2089) categories. In addition to visual inspection of anthers, pollen-staining techniques and scanning electron microscopy (SEM) analysis were used to confirm pollen sterility. Further, given the relevance of the plant mitochondrial genome to CMS manifestation, 25 mitochondrion-specific DNA markers were assayed on these newly developed A lines and isogenic maintainer (B) lines. DNA polymorphism between Pusa 992A and Pusa 992B as revealed by the nad7a_delmarker confirmed the successful combination of sterilizing cytoplasm (A4) and nonrestoring nuclear background (Pusa 992). Such cytoplasm-specific DNA markers are required for A2-CMS as well. Further, to assess restoration ability, potential restorers were crossed with these CMS lines, and as a consequence, promising A×R combinations exhibiting 100% pollen fertility could be identified. In parallel, we also analyzed the inheritance patterns underlying fertility restoration using ICPL 88039A-derived F2and BC1F1populations, and established a monogenic dominant model to explain the phenomenon of A2-CMS restoration. In summary, we report the successful development of new CMS lines and describe their effective deployment in hybrid breeding of pigeonpea.

Wheat (Triticum aestivum) is among the most important staple crops for safeguarding the food security of the growing world population. To bridge the gap between genebank diversity and breeding programs, we developed an advanced backcross–nested association mapping plus inter-crossed population (AB–NAMIC) by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection. Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB–NAMIC population. We performed phenotyping of 590 AB–NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array. Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB–NAMIC. Notably, genome-wide association studies in AB–NAMIC detected the candidate gene TaSWEET6-7B(TraesCS7B03G1216700), which has high homology to the rice SWEET6bgene and exerts strong effects on adaptation and yield traits. The commercial release of two derived AB–NAMIC lines attests to its direct applicability in wheat improvement. Valuable information on genome-wide association study mapping, candidate genes, and their haplotypes for breeding traits are available through WheatGAB (www.wheatgab.com). Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.

Grass pea offers an attractive choice for sustainable food production, owing to its intrinsic properties including limited water requirement and drought tolerance. However, low productivity and the presence of a neurotoxin (ODAP) have posed major obstacles to its genetic improvement. Also, biotechnological investments remain limited and the genome is complex and not well understood. Strategies that allow identification of genotypes with reduced ODAP content, coupling of low ODAP content with enhanced yield, and effective seed detoxification methods merit immediate attention. Breeder-friendly genomic tools are being increasingly made available to improve the efficiency of breeding protocols. To this end, the application of next-generation sequencing has provided a means of leveraging the repertoire of genomic resources for this somewhat neglected crop. In this review, we describe progress achieved in Lathyrusgenetic improvement. We also explore potential opportunities in Lathyrusresearch and identify urgent research needs.

This study reports genome wide characterization and development of first set of microsatellite markers through in silico analysis of eight sequenced Xanthomonas axonopodispv. punicaestrains available in the public database. SSR survey resulted in identification of ~ 4638 perfect SSRs, with mean marker frequency 901 SSRs/Mb and densitiy of 11,006 bp/Mb aross the eight genomes. Frequency distribution graphs revealed hexa-nucleotide repeats were more prominent fowllowed by tri-, tetra-, di- and penta-nucleotides in the analysed genomes. We desinged 2927 SSR primers that are specific to the strain LMG 859 and ePCR confirmed on seven other Xapgenomes. This resulted in identification of 542 informative SSRs that are producing single amplicons, from which 66 primers were successfully validated through wet lab experiments on eight Xapisolates of pomegranate. Furthermore, utility of these SSRs were demostrated by analysing molecular diversity among 22 Xapisolates using 20 Xap_SSR primers. SSRs revealed moderate genetic diversity among Xapisolates (61%) and grouped 11 isolates that are repersenting six different states into one cluster. This proved the earlier evidence of wider spread of ST3 type Xap acoss India using Multi locus Sequence Typing (MLST) technique. In summary, Xap_SSR will serve as powerful genomics tools that would helps in monitoring of population dynamics, taxonomy, epidomology and quarantine aspects in bacterial blight pathogen through development of microsatellite based Multilocus Variable number of Tandem repeat analysis (MLVA) in future.